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/7787277/working'
mkdir: created directory `/scratch/stefan/7787277/working/protonate'
Storing results in /scratch/stefan/7787277/finished
Working in /scratch/stefan/7787277/working
/scratch/stefan/7787277/working /scratch/stefan/7787277

/scratch/stefan/7787277/working/protonate /scratch/stefan/7787277/working /scratch/stefan/7787277
Precomputing protomers for all compounds (pH: 7.4)
rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory
mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory
rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory
mv: cannot move `/nfs/home/stefan/.install4j_new' to `/nfs/home/stefan/.install4j': No such file or directory
ph 7.4: 1048 protomers created
Coalesing and merging protomers
1025 protomers generated for 1000 compounds
Checking for new stereocenters and expanding
1041 protomers after new stereo-center expansion
/scratch/stefan/7787277/working /scratch/stefan/7787277

Bulk generating 3D conformations all protomers in /scratch/stefan/7787277/working/3D
mkdir: created directory `/scratch/stefan/7787277/working/3D'
We are using corina for 3D embeding
debuging info:: /scratch/stefan/7787277/working/protonate/xaaabsm-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'
1042 3D conformations generated for 1000 compounds

Building REAL300025497150
mkdir: created directory `/scratch/stefan/7787277/working/building'
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497150'
/scratch/stefan/7787277/working/building/REAL300025497150 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497150

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497150/0 /scratch/stefan/7787277/working/building/REAL300025497150 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1
`/scratch/stefan/7787277/working/3D/1' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CO)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497150.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497150.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497150/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497150 none CC1(CNC(=O)CO)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', '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, 12, 5, 5, 15, 15, 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, 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]
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, 105, 105, 172, 201, 201, 201, 201, 105, 105, 105, 105, 105, 91, 43, 91, 13, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 172, 172, 201, 201, 201, 603, 105, 105, 105, 105, 43, 43, 1] 603
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])
total number of confs: 1377
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497150 none CC1(CNC(=O)CO)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', '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, 12, 5, 5, 15, 15, 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, 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]
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, 24, 24, 24, 53, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 25, 105, 105, 105, 105, 105, 2, 2, 2, 6, 6, 24, 53, 53, 159, 1, 1, 1, 1, 11, 11, 105] 603
rigid atoms, others: [0, 1, 2, 34, 36, 33, 8, 9, 10, 11, 12, 13, 14, 35] set([3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39])
total number of confs: 522
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497150 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497150
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `/scratch/stefan/7787277/finished'
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497150/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497150
Building REAL300025497151
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497151'
/scratch/stefan/7787277/working/building/REAL300025497151 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497151

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497151/0 /scratch/stefan/7787277/working/building/REAL300025497151 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 2)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/2
`/scratch/stefan/7787277/working/3D/2' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497151.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497151.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497151/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497151 none CC(O)C(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 4, 7, 6, 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]
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, 197, 201, 197, 197, 143, 86, 86, 86, 86, 86, 86, 86, 86, 79, 43, 79, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 603, 197, 143, 143, 86, 86, 86, 86, 86, 86, 86, 43, 43, 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: 1375
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497151 none CC(O)C(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 4, 7, 6, 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]
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: [54, 22, 54, 22, 22, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 20, 86, 86, 86, 86, 86, 54, 54, 54, 54, 162, 22, 6, 6, 2, 2, 2, 1, 1, 1, 1, 9, 9, 86] 603
rigid atoms, others: [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, 34, 35, 40, 41, 42])
total number of confs: 496
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497151 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497151
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497151/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497151
Building REAL300025497152
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497152'
/scratch/stefan/7787277/working/building/REAL300025497152 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497152

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497152/0 /scratch/stefan/7787277/working/building/REAL300025497152 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 3)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/3
`/scratch/stefan/7787277/working/3D/3' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2CC2F)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497152.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497152.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497152/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497152 none CC1(CNC(=O)C2CC2F)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 5, 15, 5, 5, 15, 15, 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: [58, 38, 10, 10, 1, 10, 1, 1, 1, 1, 58, 58, 58, 58, 58, 58, 58, 58, 58, 85, 137, 201, 201, 201, 201, 201, 58, 58, 58, 38, 38, 10, 1, 1, 1, 1, 58, 58, 58, 58, 85, 85, 201] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9] 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, 31, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 541
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497152 none CC1(CNC(=O)C2CC2F)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 5, 15, 5, 5, 15, 15, 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: [55, 55, 55, 93, 147, 147, 147, 201, 201, 201, 55, 55, 55, 55, 55, 55, 39, 55, 13, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 93, 93, 147, 201, 201, 201, 201, 55, 55, 55, 55, 39, 39, 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: 769
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497152 none CC1(CNC(=O)C2CC2F)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 5, 15, 5, 5, 15, 15, 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, 20, 20, 20, 58, 58, 58, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 13, 55, 55, 55, 55, 55, 2, 2, 2, 6, 6, 20, 58, 58, 58, 58, 1, 1, 1, 1, 6, 6, 55] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 16] set([3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
total number of confs: 245
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497152 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497152
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497152/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497152
Building REAL300025497153
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497153'
/scratch/stefan/7787277/working/building/REAL300025497153 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497153

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497153/0 /scratch/stefan/7787277/working/building/REAL300025497153 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 4)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/4
`/scratch/stefan/7787277/working/3D/4' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CCF)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497153.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497153.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497153/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497153 none CC1(CNC(=O)CCF)CC(F)(F)CN1C(=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', 'F', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 15, 5, 5, 15, 15, 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
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, 79, 121, 121, 121, 201, 201, 48, 48, 48, 48, 48, 48, 35, 48, 13, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 79, 79, 121, 201, 201, 201, 201, 48, 48, 48, 48, 35, 35, 1] 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])
total number of confs: 878
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497153 none CC1(CNC(=O)CCF)CC(F)(F)CN1C(=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', 'F', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 15, 5, 5, 15, 15, 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
201  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, 11, 11, 11, 52, 66, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 48, 48, 48, 48, 48, 2, 2, 2, 4, 4, 11, 52, 52, 66, 66, 1, 1, 1, 1, 5, 5, 48] 201
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15] set([3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41])
total number of confs: 345
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497153 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497153
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497153/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497153
Building REAL300025497154
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497154'
/scratch/stefan/7787277/working/building/REAL300025497154 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497154

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497154/0 /scratch/stefan/7787277/working/building/REAL300025497154 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 5)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/5
`/scratch/stefan/7787277/working/3D/5' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C=CCF)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497154.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497154.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497154/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497154 none CC1(CNC(=O)C=CCF)CC(F)(F)CN1C(=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', 'F', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 15, 5, 5, 15, 15, 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
172  conformations in input
total number of sets (complete confs): 172
using faster count positions algorithm for large data
unique positions, atoms: [67, 67, 67, 96, 117, 117, 117, 172, 172, 172, 67, 67, 67, 67, 67, 64, 43, 64, 13, 1, 1, 1, 1, 1, 1, 1, 67, 67, 67, 96, 96, 117, 172, 172, 172, 172, 67, 67, 67, 67, 43, 43, 1] 172
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: 677
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497154 none CC1(CNC(=O)C=CCF)CC(F)(F)CN1C(=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', 'F', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 5, 15, 5, 5, 15, 15, 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
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, 4, 7, 7, 7, 37, 37, 89, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 17, 67, 67, 67, 67, 67, 2, 2, 2, 4, 4, 7, 37, 37, 89, 89, 1, 1, 1, 1, 7, 7, 67] 172
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 16] set([3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
total number of confs: 426
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497154 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497154
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497154/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497154
Building REAL300025497155
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497155'
/scratch/stefan/7787277/working/building/REAL300025497155 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497155

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497155/0 /scratch/stefan/7787277/working/building/REAL300025497155 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 6)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/6
`/scratch/stefan/7787277/working/3D/6' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCC(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497155.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497155.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497155/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497155 none C#CCCC(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 7, 7, 6, 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]
0  hydrogens need rotated
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, 120, 120, 120, 103, 63, 63, 63, 63, 63, 63, 63, 63, 58, 32, 58, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 198, 198, 120, 103, 103, 63, 63, 63, 63, 63, 63, 63, 32, 32, 1] 201
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: 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: REAL300025497155 none C#CCCC(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 7, 7, 6, 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]
0  hydrogens 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, 35, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 63, 63, 63, 63, 63, 48, 48, 48, 35, 35, 7, 4, 4, 2, 2, 2, 1, 1, 1, 1, 6, 6, 63] 201
rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 39] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43])
total number of confs: 295
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497155 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497155
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497155/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497155
Building REAL300025497156
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497156'
/scratch/stefan/7787277/working/building/REAL300025497156 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497156

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497156/0 /scratch/stefan/7787277/working/building/REAL300025497156 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 7)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/7
`/scratch/stefan/7787277/working/3D/7' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#C[C@H]1C[C@H]1C(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497156.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497156.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497156/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497156 none C#C[C@H]1C[C@H]1C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', '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: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 30, 8, 30, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 15, 78, 78, 78, 78, 78, 30, 30, 30, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 7, 7, 78] 201
rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497156 none C#C[C@H]1C[C@H]1C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', '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: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 152, 201, 152, 152, 123, 78, 78, 78, 78, 78, 78, 78, 78, 71, 32, 71, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 152, 123, 123, 78, 78, 78, 78, 78, 78, 78, 32, 32, 1] 201
rigid atoms, others: [44, 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])
total number of confs: 776
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497156 none C#C[C@H]1C[C@H]1C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', '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: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 30, 30, 30, 30, 30, 30, 30, 30, 35, 35, 79, 127, 201, 201, 201, 201, 201, 1, 1, 1, 8, 21, 21, 30, 30, 30, 30, 30, 30, 30, 79, 79, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 550
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497156 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497156
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497156/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497156
Building REAL300025497157
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497157'
/scratch/stefan/7787277/working/building/REAL300025497157 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497157

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497157/0 /scratch/stefan/7787277/working/building/REAL300025497157 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 8)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/8
`/scratch/stefan/7787277/working/3D/8' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2CCO2)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497157.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497157.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497157/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497157 none CC1(CNC(=O)C2CCO2)CC(F)(F)CN1C(=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', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 5, 12, 5, 5, 15, 15, 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, 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]
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: [28, 19, 9, 9, 1, 9, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 30, 30, 59, 67, 96, 96, 96, 96, 96, 28, 28, 28, 19, 19, 9, 1, 1, 1, 1, 1, 28, 28, 28, 28, 59, 59, 96] 96
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 36] 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, 31, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 296
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497157 none CC1(CNC(=O)C2CCO2)CC(F)(F)CN1C(=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', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 5, 12, 5, 5, 15, 15, 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, 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]
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: [65, 65, 65, 91, 95, 95, 95, 96, 96, 96, 65, 65, 65, 65, 65, 64, 37, 64, 13, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 91, 91, 95, 96, 96, 96, 96, 96, 65, 65, 65, 65, 37, 37, 1] 96
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: 379
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497157 none CC1(CNC(=O)C2CCO2)CC(F)(F)CN1C(=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', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 5, 12, 5, 5, 15, 15, 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, 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]
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, 7, 14, 14, 14, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 22, 65, 65, 65, 65, 65, 2, 2, 2, 7, 7, 14, 28, 28, 28, 28, 28, 1, 1, 1, 1, 12, 12, 65] 96
rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16] set([3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43])
total number of confs: 201
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497157 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497157
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497157/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497157
Building REAL300025497158
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497158'
/scratch/stefan/7787277/working/building/REAL300025497158 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497158

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497158/0 /scratch/stefan/7787277/working/building/REAL300025497158 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 9)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/9
`/scratch/stefan/7787277/working/3D/9' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(O)C(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497158.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497158.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497158/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497158 none CC(C)(O)C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 199, 201, 201, 199, 199, 128, 70, 70, 70, 70, 70, 70, 70, 70, 70, 42, 70, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 199, 128, 128, 70, 70, 70, 70, 70, 70, 70, 42, 42, 1] 603
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: 1388
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497158 none CC(C)(O)C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [57, 21, 57, 57, 21, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 13, 70, 70, 70, 70, 70, 57, 57, 57, 57, 57, 57, 171, 21, 6, 6, 2, 2, 2, 1, 1, 1, 1, 6, 6, 70] 603
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45])
total number of confs: 491
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497158 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497158
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497158/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497158
Building REAL300025497159
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497159'
/scratch/stefan/7787277/working/building/REAL300025497159 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497159

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497159/0 /scratch/stefan/7787277/working/building/REAL300025497159 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 10)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/10
`/scratch/stefan/7787277/working/3D/10' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC1C(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497159.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497159.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497159/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497159 none CC1=CC1C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 7, 7, 6, 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]
0  hydrogens 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, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 15, 76, 76, 76, 76, 76, 47, 47, 47, 47, 47, 7, 4, 4, 2, 2, 2, 1, 1, 1, 1, 7, 7, 76] 201
rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 39] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43])
total number of confs: 231
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497159 none CC1=CC1C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 7, 7, 6, 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]
0  hydrogens need rotated
201  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, 128, 128, 116, 76, 76, 76, 76, 76, 76, 76, 76, 69, 31, 69, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 128, 116, 116, 76, 76, 76, 76, 76, 76, 76, 31, 31, 1] 201
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: 742
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497159 none CC1=CC1C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 31, 47, 47, 47, 47, 47, 47, 47, 47, 54, 54, 94, 146, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 13, 31, 31, 47, 47, 47, 47, 47, 47, 47, 94, 94, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 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, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 600
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497159 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497159
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497159/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497159
Building REAL300025497160
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497160'
/scratch/stefan/7787277/working/building/REAL300025497160 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497160

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497160/0 /scratch/stefan/7787277/working/building/REAL300025497160 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 11)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/11
`/scratch/stefan/7787277/working/3D/11' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497160.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497160.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497160/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497160 none C[C@@H](O)C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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]
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, 201, 198, 198, 127, 102, 102, 102, 102, 102, 102, 102, 102, 81, 43, 81, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 603, 198, 127, 127, 102, 102, 102, 102, 102, 102, 102, 43, 43, 1] 603
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: 1304
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497160 none C[C@@H](O)C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [34, 12, 34, 34, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 25, 102, 102, 102, 102, 102, 34, 34, 34, 102, 12, 4, 4, 2, 2, 2, 1, 1, 1, 1, 10, 10, 102] 603
rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 39] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
total number of confs: 392
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497160 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497160
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497160/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497160
Building REAL300025497161
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497161'
/scratch/stefan/7787277/working/building/REAL300025497161 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497161

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497161/0 /scratch/stefan/7787277/working/building/REAL300025497161 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 12)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/12
`/scratch/stefan/7787277/working/3D/12' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C=CCO)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497161.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497161.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497161/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497161 none CC1(CNC(=O)C=CCO)CC(F)(F)CN1C(=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', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 12, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 107, 125, 125, 125, 201, 201, 201, 75, 75, 75, 75, 75, 72, 45, 72, 13, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 107, 107, 125, 201, 201, 201, 201, 603, 75, 75, 75, 75, 45, 45, 1] 603
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: 1385
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: REAL300025497161 none CC1(CNC(=O)C=CCO)CC(F)(F)CN1C(=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', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 12, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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]
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, 37, 37, 94, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 17, 75, 75, 75, 75, 75, 2, 2, 2, 4, 4, 7, 37, 37, 94, 94, 282, 1, 1, 1, 1, 7, 7, 75] 603
rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16] set([3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43])
total number of confs: 731
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497161 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497161
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497161/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497161
Building REAL300025497162
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497162'
/scratch/stefan/7787277/working/building/REAL300025497162 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497162

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497162/0 /scratch/stefan/7787277/working/building/REAL300025497162 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 13)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/13
`/scratch/stefan/7787277/working/3D/13' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(F)C(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497162.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497162.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497162/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497162 none COC(F)C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 12, 5, 15, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 3, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 147, 201, 147, 147, 118, 81, 81, 81, 81, 81, 81, 81, 81, 77, 32, 77, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 147, 118, 118, 81, 81, 81, 81, 81, 81, 81, 32, 32, 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: 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: REAL300025497162 none COC(F)C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 12, 5, 15, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 3, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 34, 9, 34, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 16, 81, 81, 81, 81, 81, 69, 69, 69, 34, 9, 4, 4, 2, 2, 2, 1, 1, 1, 1, 7, 7, 81] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 39] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/7787277/working/building/REAL300025497162 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497162
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497162/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497162
Building REAL300025497163
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497163'
/scratch/stefan/7787277/working/building/REAL300025497163 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497163

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497163/0 /scratch/stefan/7787277/working/building/REAL300025497163 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 14)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/14
`/scratch/stefan/7787277/working/3D/14' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2=CCC2)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497163.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497163.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497163/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497163 none CC1(CNC(=O)C2=CCC2)CC(F)(F)CN1C(=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', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 5, 5, 5, 15, 15, 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, 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]
0  hydrogens need rotated
39  conformations in input
total number of sets (complete confs): 39
using default count positions algorithm for smaller data
unique positions, atoms: [12, 9, 6, 6, 1, 6, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 22, 25, 39, 39, 39, 39, 39, 12, 12, 12, 9, 9, 6, 1, 1, 1, 1, 1, 12, 12, 12, 12, 22, 22, 39] 39
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 36] 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, 31, 37, 38, 39, 40, 41, 42, 43])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497163 none CC1(CNC(=O)C2=CCC2)CC(F)(F)CN1C(=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', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 5, 5, 5, 15, 15, 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, 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]
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: [34, 34, 34, 39, 39, 39, 39, 39, 39, 39, 34, 34, 34, 34, 34, 34, 28, 34, 12, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 39, 39, 39, 39, 39, 39, 39, 39, 34, 34, 34, 34, 28, 28, 1] 39
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: 141
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497163 none CC1(CNC(=O)C2=CCC2)CC(F)(F)CN1C(=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', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 5, 5, 5, 15, 15, 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, 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]
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, 4, 4, 4, 4, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 12, 34, 34, 34, 34, 34, 2, 2, 2, 4, 4, 4, 12, 12, 12, 12, 12, 1, 1, 1, 1, 7, 7, 34] 39
rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16] set([3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43])
total number of confs: 92
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497163 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497163
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497163/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497163
Building REAL300025497164
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497164'
/scratch/stefan/7787277/working/building/REAL300025497164 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497164

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497164/0 /scratch/stefan/7787277/working/building/REAL300025497164 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 15)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/15
`/scratch/stefan/7787277/working/3D/15' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=CC(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497164.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497164.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497164/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497164 none CON=CC(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 3, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  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, 198, 198, 175, 97, 97, 97, 97, 97, 97, 97, 97, 86, 34, 86, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 198, 175, 175, 97, 97, 97, 97, 97, 97, 97, 34, 34, 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: 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: REAL300025497164 none CON=CC(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 12, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 3, 7, 7, 7, 6, 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]
0  hydrogens 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, 34, 34, 15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 20, 97, 97, 97, 97, 97, 44, 44, 44, 34, 15, 7, 7, 2, 2, 2, 1, 1, 1, 1, 10, 10, 97] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 39] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
total number of confs: 269
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497164 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497164
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497164/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497164
Building REAL300025497165
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497165'
/scratch/stefan/7787277/working/building/REAL300025497165 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497165

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497165/0 /scratch/stefan/7787277/working/building/REAL300025497165 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 16)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/16
`/scratch/stefan/7787277/working/3D/16' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2(F)CC2)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497165.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497165.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497165/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497165 none CC1(CNC(=O)C2(F)CC2)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 15, 5, 5, 5, 5, 15, 15, 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: [61, 38, 10, 10, 1, 10, 1, 1, 1, 1, 61, 61, 61, 61, 61, 61, 61, 61, 61, 88, 123, 201, 201, 201, 201, 201, 61, 61, 61, 38, 38, 10, 1, 1, 1, 1, 61, 61, 61, 61, 88, 88, 201] 201
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9] 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, 31, 36, 37, 38, 39, 40, 41, 42])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497165 none CC1(CNC(=O)C2(F)CC2)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 15, 5, 5, 5, 5, 15, 15, 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: [66, 66, 66, 110, 164, 164, 164, 201, 201, 201, 66, 66, 66, 66, 66, 66, 43, 66, 13, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 110, 110, 164, 201, 201, 201, 201, 66, 66, 66, 66, 43, 43, 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: 777
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497165 none CC1(CNC(=O)C2(F)CC2)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 15, 5, 5, 5, 5, 15, 15, 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, 19, 19, 19, 61, 61, 61, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 14, 66, 66, 66, 66, 66, 2, 2, 2, 6, 6, 19, 61, 61, 61, 61, 1, 1, 1, 1, 7, 7, 66] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 16] set([3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
total number of confs: 271
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497165 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497165
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497165/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497165
Building REAL300025497166
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497166'
/scratch/stefan/7787277/working/building/REAL300025497166 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497166

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497166/0 /scratch/stefan/7787277/working/building/REAL300025497166 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 17)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/17
`/scratch/stefan/7787277/working/3D/17' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(F)C(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497166.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497166.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497166/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497166 none CC=C(F)C(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
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, 201, 178, 178, 163, 98, 98, 98, 98, 98, 98, 98, 98, 77, 31, 77, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 178, 163, 163, 98, 98, 98, 98, 98, 98, 98, 31, 31, 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: 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: REAL300025497166 none CC=C(F)C(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 1, 1, 15, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 12, 34, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 24, 98, 98, 98, 98, 98, 34, 34, 34, 34, 12, 6, 6, 2, 2, 2, 1, 1, 1, 1, 13, 13, 98] 201
rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 39] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
total number of confs: 256
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497166 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497166
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497166/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497166
Building REAL300025497167
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497167'
/scratch/stefan/7787277/working/building/REAL300025497167 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497167

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497167/0 /scratch/stefan/7787277/working/building/REAL300025497167 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 18)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/18
`/scratch/stefan/7787277/working/3D/18' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CO)C(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497167.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497167.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497167/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497167 none CC(CO)C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 147, 201, 201, 147, 147, 121, 73, 73, 73, 73, 73, 73, 73, 73, 71, 31, 71, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 603, 147, 121, 121, 73, 73, 73, 73, 73, 73, 73, 31, 31, 1] 603
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: 1493
number of broken/clashed sets: 96
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497167 none CC(CO)C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 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: [33, 8, 33, 53, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 15, 73, 73, 73, 73, 73, 33, 33, 33, 33, 53, 53, 159, 8, 4, 4, 2, 2, 2, 1, 1, 1, 1, 7, 7, 73] 603
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45])
total number of confs: 486
number of broken/clashed sets: 96
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497167 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497167
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497167/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497167
Building REAL300025497168
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497168'
/scratch/stefan/7787277/working/building/REAL300025497168 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497168

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497168/0 /scratch/stefan/7787277/working/building/REAL300025497168 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 19)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/19
`/scratch/stefan/7787277/working/3D/19' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC1(C(=O)NCC2(C)CC(F)(F)CN2C(=O)CSC2=NNC(=O)[N-]2)CC1)

`REAL300025497168.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497168.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497168/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497168 none C#CC1(C(=O)NCC2(C)CC(F)(F)CN2C(=O)CSC2=NNC(=O)[N-]2)CC1 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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 6, 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, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 19, 74, 74, 74, 74, 74, 29, 29, 29, 7, 4, 4, 2, 2, 2, 1, 1, 1, 1, 10, 10, 74, 29, 29, 29, 29] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 203
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497168 none C#CC1(C(=O)NCC2(C)CC(F)(F)CN2C(=O)CSC2=NNC(=O)[N-]2)CC1 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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 6, 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, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 105, 105, 105, 101, 74, 74, 74, 74, 74, 74, 74, 74, 60, 31, 60, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 105, 101, 101, 74, 74, 74, 74, 74, 74, 74, 31, 31, 1, 201, 201, 201, 201] 201
rigid atoms, others: [40, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44])
total number of confs: 679
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497168 none C#CC1(C(=O)NCC2(C)CC(F)(F)CN2C(=O)CSC2=NNC(=O)[N-]2)CC1 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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 7, 6, 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, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 18, 29, 29, 29, 29, 29, 29, 29, 29, 34, 34, 73, 115, 201, 201, 201, 201, 201, 1, 1, 1, 7, 18, 18, 29, 29, 29, 29, 29, 29, 29, 73, 73, 201, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 41, 42, 43, 44, 25, 26, 27] set([4, 5, 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])
total number of confs: 534
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497168 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497168
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497168/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497168
Building REAL300025497169
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497169'
/scratch/stefan/7787277/working/building/REAL300025497169 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497169

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497169/0 /scratch/stefan/7787277/working/building/REAL300025497169 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 20)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/20
`/scratch/stefan/7787277/working/3D/20' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497169.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497169.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497169/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497169 none C[C@H](O)C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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]
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, 201, 198, 198, 121, 96, 96, 96, 96, 96, 96, 96, 96, 75, 43, 75, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 603, 198, 121, 121, 96, 96, 96, 96, 96, 96, 96, 43, 43, 1] 603
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: 1303
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497169 none C[C@H](O)C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.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, 7, 12, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 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]
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: [35, 12, 35, 35, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 25, 96, 96, 96, 96, 96, 35, 35, 35, 105, 12, 4, 4, 2, 2, 2, 1, 1, 1, 1, 10, 10, 96] 603
rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 39] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
total number of confs: 394
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497169 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497169
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497169/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497169
Building REAL300025497170
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497170'
/scratch/stefan/7787277/working/building/REAL300025497170 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497170

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497170/0 /scratch/stefan/7787277/working/building/REAL300025497170 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 21)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/21
`/scratch/stefan/7787277/working/3D/21' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC1C(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497170.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497170.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497170/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497170 none C=C1CC1C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 7, 7, 6, 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]
0  hydrogens 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, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 71, 71, 71, 71, 71, 44, 44, 44, 44, 44, 9, 4, 4, 2, 2, 2, 1, 1, 1, 1, 7, 7, 71] 201
rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 39] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43])
total number of confs: 218
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497170 none C=C1CC1C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 117, 117, 117, 107, 71, 71, 71, 71, 71, 71, 71, 71, 64, 31, 64, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 117, 107, 107, 71, 71, 71, 71, 71, 71, 71, 31, 31, 1] 201
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: 724
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497170 none C=C1CC1C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 13, 13, 13, 31, 44, 44, 44, 44, 44, 44, 44, 44, 50, 50, 90, 132, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 13, 31, 31, 44, 44, 44, 44, 44, 44, 44, 90, 90, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 26, 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, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 587
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497170 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497170
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497170/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497170
Building REAL300025497171
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497171'
/scratch/stefan/7787277/working/building/REAL300025497171 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497171

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497171/0 /scratch/stefan/7787277/working/building/REAL300025497171 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 22)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/22
`/scratch/stefan/7787277/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)CC(F)(F)CN1C(=O)CC1CC1)

`REAL300025497171.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497171.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497171/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497171 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 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, 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
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [97, 76, 59, 59, 28, 59, 13, 1, 1, 1, 1, 1, 1, 1, 97, 97, 97, 97, 97, 97, 97, 98, 98, 135, 142, 142, 97, 97, 97, 76, 76, 59, 28, 28, 1, 97, 97, 97, 97, 135, 135, 142, 142, 142, 142, 142] 142
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: 609
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497171 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 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, 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
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 27, 48, 48, 48, 110, 117, 142, 142, 142, 142, 142, 13, 13, 13, 13, 13, 13, 3, 13, 1, 1, 1, 1, 13, 13, 13, 27, 27, 48, 110, 110, 142, 13, 13, 13, 13, 3, 3, 1, 1, 1, 1, 1] 142
rigid atoms, others: [41, 42, 43, 44, 45, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 499
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497171 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 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, 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
142  conformations in input
total number of sets (complete confs): 142
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 10, 10, 10, 37, 44, 97, 97, 97, 97, 97, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 13, 13, 2, 2, 2, 5, 5, 10, 37, 37, 97, 1, 1, 1, 1, 9, 9, 13, 13, 13, 13, 13] 142
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 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, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 269
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497171 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497171
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497171/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497171
Building REAL300025497172
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497172'
/scratch/stefan/7787277/working/building/REAL300025497172 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497172

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497172/0 /scratch/stefan/7787277/working/building/REAL300025497172 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 23)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/23
`/scratch/stefan/7787277/working/3D/23' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(F)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497172.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497172.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497172/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497172 none CC(C)(F)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 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
125  conformations in input
total number of sets (complete confs): 125
using faster count positions algorithm for large data
unique positions, atoms: [125, 125, 125, 125, 124, 125, 124, 124, 124, 124, 124, 124, 115, 124, 77, 77, 31, 77, 12, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 125, 125, 124, 124, 124, 124, 124, 124, 124, 115, 115, 77, 31, 31, 1] 125
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: 475
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497172 none CC(C)(F)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 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
125  conformations in input
total number of sets (complete confs): 125
using faster count positions algorithm for large data
unique positions, atoms: [4, 3, 4, 4, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 65, 82, 124, 124, 124, 124, 124, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 6, 6, 20, 65, 65, 124] 125
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 5, 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])
total number of confs: 358
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497172 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497172
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497172/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497172
Building REAL300025497173
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497173'
/scratch/stefan/7787277/working/building/REAL300025497173 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497173

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497173/0 /scratch/stefan/7787277/working/building/REAL300025497173 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 24)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/24
`/scratch/stefan/7787277/working/3D/24' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(F)(F)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497173.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497173.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497173/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497173 none CC(F)(F)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 15, 15, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [119, 112, 119, 119, 112, 112, 112, 112, 112, 112, 112, 112, 102, 112, 74, 74, 34, 74, 13, 1, 1, 1, 1, 1, 1, 1, 119, 119, 119, 112, 112, 112, 112, 112, 112, 112, 102, 102, 74, 34, 34, 1] 119
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: 458
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497173 none CC(F)(F)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 15, 15, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
119  conformations in input
total number of sets (complete confs): 119
using faster count positions algorithm for large data
unique positions, atoms: [5, 3, 5, 5, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20, 20, 57, 70, 112, 112, 112, 112, 112, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 6, 6, 20, 57, 57, 112] 119
rigid atoms, others: [32, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 325
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497173 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497173
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497173/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497173
Building REAL300025497174
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497174'
/scratch/stefan/7787277/working/building/REAL300025497174 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497174

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497174/0 /scratch/stefan/7787277/working/building/REAL300025497174 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 25)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/25
`/scratch/stefan/7787277/working/3D/25' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497174.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497174.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497174/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497174 none COCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 15, 15, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [81, 81, 59, 59, 59, 59, 59, 59, 59, 59, 59, 47, 59, 30, 30, 17, 30, 11, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 59, 59, 59, 59, 59, 59, 59, 47, 47, 30, 17, 17, 1] 81
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: 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: REAL300025497174 none COCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 15, 15, 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, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [23, 11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 28, 28, 59, 59, 59, 59, 59, 23, 23, 23, 11, 11, 1, 1, 1, 1, 2, 2, 2, 3, 3, 8, 28, 28, 59] 81
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 212
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497174 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497174
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497174/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497174
Building REAL300025497175
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497175'
/scratch/stefan/7787277/working/building/REAL300025497175 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497175

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497175/0 /scratch/stefan/7787277/working/building/REAL300025497175 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 26)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/26
`/scratch/stefan/7787277/working/3D/26' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497175.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497175.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497175/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497175 none CCCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [130, 130, 101, 101, 101, 101, 101, 101, 101, 101, 101, 83, 101, 56, 56, 26, 56, 13, 1, 1, 1, 1, 1, 1, 1, 130, 130, 130, 130, 130, 130, 130, 101, 101, 101, 101, 101, 101, 101, 83, 83, 56, 26, 26, 1] 130
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: 551
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497175 none CCCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
130  conformations in input
total number of sets (complete confs): 130
using faster count positions algorithm for large data
unique positions, atoms: [9, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 42, 49, 101, 101, 101, 101, 101, 10, 10, 10, 10, 10, 7, 7, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 42, 42, 101] 130
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35] set([0, 1, 2, 4, 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])
total number of confs: 293
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497175 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497175
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497175/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497175
Building REAL300025497176
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497176'
/scratch/stefan/7787277/working/building/REAL300025497176 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497176

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497176/0 /scratch/stefan/7787277/working/building/REAL300025497176 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 27)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/27
`/scratch/stefan/7787277/working/3D/27' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497176.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497176.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497176/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497176 none CC(C)CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [81, 81, 81, 66, 66, 66, 66, 66, 66, 66, 66, 66, 61, 66, 50, 50, 24, 50, 11, 1, 1, 1, 1, 1, 1, 1, 81, 81, 81, 81, 81, 81, 81, 81, 81, 66, 66, 66, 66, 66, 66, 66, 61, 61, 50, 24, 24, 1] 81
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: 330
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497176 none CC(C)CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
81  conformations in input
total number of sets (complete confs): 81
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 36, 41, 66, 66, 66, 66, 66, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 4, 4, 11, 36, 36, 66] 81
rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36, 38] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 193
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497176 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497176
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497176/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497176
Building REAL300025497177
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497177'
/scratch/stefan/7787277/working/building/REAL300025497177 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497177

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497177/0 /scratch/stefan/7787277/working/building/REAL300025497177 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 28)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/28
`/scratch/stefan/7787277/working/3D/28' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497177.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497177.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497177/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497177 none CC1CC1C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 36, 41, 71, 71, 71, 71, 71, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 36, 36, 71] 91
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497177 none CC1CC1C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 72, 71, 72, 71, 71, 71, 71, 71, 71, 59, 71, 47, 47, 27, 47, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 91, 91, 71, 71, 71, 71, 71, 71, 71, 59, 59, 47, 27, 27, 1] 91
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: 344
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497177 none CC1CC1C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 16, 32, 32, 32, 68, 73, 91, 91, 91, 91, 91, 2, 2, 2, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 16, 16, 32, 68, 68, 91] 91
rigid atoms, others: [0, 1, 2, 3, 4, 32, 29, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 308
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497177 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497177
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497177/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497177
Building REAL300025497178
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497178'
/scratch/stefan/7787277/working/building/REAL300025497178 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497178

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497178/0 /scratch/stefan/7787277/working/building/REAL300025497178 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 29)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/29
`/scratch/stefan/7787277/working/3D/29' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497178.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497178.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497178/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497178 none CCOCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 140, 139, 140, 139, 139, 139, 139, 139, 139, 106, 139, 62, 62, 29, 62, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 195, 195, 139, 139, 139, 139, 139, 139, 139, 106, 106, 62, 29, 29, 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: 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: REAL300025497178 none CCOCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 33, 51, 139, 139, 139, 139, 139, 18, 18, 18, 18, 18, 7, 7, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 33, 33, 139] 201
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 329
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497178 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497178
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497178/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497178
Building REAL300025497179
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497179'
/scratch/stefan/7787277/working/building/REAL300025497179 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497179

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497179/0 /scratch/stefan/7787277/working/building/REAL300025497179 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 30)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/30
`/scratch/stefan/7787277/working/3D/30' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497179.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497179.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497179/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497179 none CC(C)=CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [80, 80, 80, 67, 67, 67, 67, 67, 67, 67, 67, 67, 60, 67, 47, 47, 25, 47, 12, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 80, 80, 67, 67, 67, 67, 67, 67, 67, 60, 60, 47, 25, 25, 1] 80
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: 299
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497179 none CC(C)=CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
80  conformations in input
total number of sets (complete confs): 80
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 36, 41, 67, 67, 67, 67, 67, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 36, 36, 67] 80
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 200
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497179 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497179
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497179/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497179
Building REAL300025497180
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497180'
/scratch/stefan/7787277/working/building/REAL300025497180 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497180

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497180/0 /scratch/stefan/7787277/working/building/REAL300025497180 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 31)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/31
`/scratch/stefan/7787277/working/3D/31' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497180.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497180.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497180/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497180 none CSCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [108, 89, 59, 59, 59, 59, 59, 59, 59, 59, 59, 49, 59, 31, 31, 20, 31, 12, 1, 1, 1, 1, 1, 1, 1, 108, 108, 108, 89, 89, 59, 59, 59, 59, 59, 59, 59, 49, 49, 31, 20, 20, 1] 108
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: 435
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497180 none CSCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
108  conformations in input
total number of sets (complete confs): 108
using faster count positions algorithm for large data
unique positions, atoms: [27, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 30, 30, 59, 59, 59, 59, 59, 27, 27, 27, 9, 9, 1, 1, 1, 1, 2, 2, 2, 3, 3, 8, 30, 30, 59] 108
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 215
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497180 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497180
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497180/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497180
Building REAL300025497181
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497181'
/scratch/stefan/7787277/working/building/REAL300025497181 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497181

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497181/0 /scratch/stefan/7787277/working/building/REAL300025497181 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 32)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/32
`/scratch/stefan/7787277/working/3D/32' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497181.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497181.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497181/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497181 none CCCCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 99, 98, 99, 98, 98, 98, 98, 98, 98, 68, 98, 44, 44, 27, 44, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 184, 184, 98, 98, 98, 98, 98, 98, 98, 68, 68, 44, 27, 27, 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: 897
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497181 none CCCCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 12, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 24, 34, 98, 98, 98, 98, 98, 21, 21, 21, 21, 20, 14, 14, 9, 9, 1, 1, 1, 1, 2, 2, 2, 5, 5, 8, 24, 24, 98] 201
rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36, 38] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 296
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497181 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497181
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497181/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497181
Building REAL300025497182
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497182'
/scratch/stefan/7787277/working/building/REAL300025497182 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497182

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497182/0 /scratch/stefan/7787277/working/building/REAL300025497182 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 33)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/33
`/scratch/stefan/7787277/working/3D/33' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497182.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497182.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497182/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497182 none CC(C)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 48, 54, 39, 39, 21, 39, 11, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 48, 48, 39, 21, 21, 1] 54
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: 193
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497182 none CC(C)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [4, 3, 4, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 35, 38, 54, 54, 54, 54, 54, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 35, 35, 54] 54
rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35] set([0, 1, 2, 4, 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])
total number of confs: 182
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497182 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497182
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497182/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497182
Building REAL300025497183
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497183'
/scratch/stefan/7787277/working/building/REAL300025497183 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497183

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497183/0 /scratch/stefan/7787277/working/building/REAL300025497183 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 34)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/34
`/scratch/stefan/7787277/working/3D/34' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497183.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497183.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497183/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497183 none CCC(C)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 68, 68, 68, 68, 68, 60, 68, 43, 43, 24, 43, 10, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 68, 60, 60, 43, 24, 24, 1] 68
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: 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: REAL300025497183 none CCC(C)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [5, 4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 30, 36, 68, 68, 68, 68, 68, 5, 5, 5, 5, 5, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 30, 30, 68] 68
rigid atoms, others: [35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36, 38] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 194
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497183 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497183
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497183/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497183
Building REAL300025497184
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497184'
/scratch/stefan/7787277/working/building/REAL300025497184 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497184

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497184/0 /scratch/stefan/7787277/working/building/REAL300025497184 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 35)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/35
`/scratch/stefan/7787277/working/3D/35' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497184.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497184.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497184/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497184 none COC(C)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 16, 17, 16, 16, 16, 16, 16, 16, 16, 16, 15, 16, 14, 14, 11, 14, 8, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 16, 16, 16, 16, 16, 16, 16, 15, 15, 14, 11, 11, 1] 17
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: 53
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497184 none COC(C)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [5, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 12, 12, 16, 16, 16, 16, 16, 5, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 8, 12, 12, 16] 17
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 68
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497184 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497184
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497184/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497184
Building REAL300025497185
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497185'
/scratch/stefan/7787277/working/building/REAL300025497185 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497185

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497185/0 /scratch/stefan/7787277/working/building/REAL300025497185 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 36)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/36
`/scratch/stefan/7787277/working/3D/36' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497185.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497185.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497185/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497185 none C=CCCC(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 125, 125, 125, 125, 125, 125, 92, 125, 56, 56, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 194, 194, 125, 125, 125, 125, 125, 125, 125, 92, 92, 56, 29, 29, 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: 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: REAL300025497185 none C=CCCC(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 8, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 26, 38, 125, 125, 125, 125, 125, 20, 20, 20, 8, 8, 7, 7, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 26, 26, 125] 201
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 308
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497185 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497185
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497185/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497185
Building REAL300025497186
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497186'
/scratch/stefan/7787277/working/building/REAL300025497186 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497186

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497186/0 /scratch/stefan/7787277/working/building/REAL300025497186 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 37)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/37
`/scratch/stefan/7787277/working/3D/37' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C#N)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497186.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497186.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497186/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497186 none CC(C#N)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [38, 35, 38, 38, 35, 35, 35, 35, 35, 35, 35, 35, 32, 35, 24, 24, 16, 24, 10, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 35, 35, 35, 35, 35, 35, 35, 32, 32, 24, 16, 16, 1] 38
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: 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: REAL300025497186 none CC(C#N)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.1', 'N.1', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 1, 8, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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
38  conformations in input
total number of sets (complete confs): 38
using default count positions algorithm for smaller data
unique positions, atoms: [5, 2, 5, 5, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 27, 27, 35, 35, 35, 35, 35, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 27, 27, 35] 38
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 139
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497186 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497186
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497186/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497186
Building REAL300025497187
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497187'
/scratch/stefan/7787277/working/building/REAL300025497187 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497187

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497187/0 /scratch/stefan/7787277/working/building/REAL300025497187 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 38)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/38
`/scratch/stefan/7787277/working/3D/38' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(C)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497187.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497187.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497187/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497187 none CC=C(C)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 90, 110, 90, 90, 90, 90, 90, 90, 90, 90, 77, 90, 59, 59, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 110, 110, 110, 110, 110, 110, 110, 90, 90, 90, 90, 90, 90, 90, 77, 77, 59, 29, 29, 1] 110
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: 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: REAL300025497187 none CC=C(C)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [8, 8, 3, 8, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 37, 47, 90, 90, 90, 90, 90, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 37, 37, 90] 110
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 247
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497187 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497187
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497187/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497187
Building REAL300025497188
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497188'
/scratch/stefan/7787277/working/building/REAL300025497188 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497188

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497188/0 /scratch/stefan/7787277/working/building/REAL300025497188 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 39)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/39
`/scratch/stefan/7787277/working/3D/39' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C#CC1CC1)

`REAL300025497188.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497188.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497188/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497188 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C#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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 1, 1, 5, 5, 5, 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, 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
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [50, 45, 36, 36, 24, 36, 11, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 51, 51, 51, 51, 51, 51, 50, 50, 50, 45, 45, 36, 24, 24, 1, 50, 50, 50, 50, 51, 51, 51, 51, 51] 51
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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497188 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C#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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 1, 1, 5, 5, 5, 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, 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
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [3, 3, 3, 6, 14, 14, 14, 35, 37, 51, 51, 51, 51, 51, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 14, 35, 35, 51, 3, 3, 3, 3, 1, 1, 1, 1, 1] 51
rigid atoms, others: [40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 155
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497188 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C#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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.1', 'C.1', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 1, 1, 5, 5, 5, 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, 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
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 13, 13, 13, 34, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 2, 2, 2, 5, 5, 13, 34, 34, 50, 1, 1, 1, 1, 3, 3, 3, 3, 3] 51
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 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, 40, 41, 42, 43, 44])
total number of confs: 167
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497188 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497188
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497188/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497188
Building REAL300025497189
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497189'
/scratch/stefan/7787277/working/building/REAL300025497189 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497189

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497189/0 /scratch/stefan/7787277/working/building/REAL300025497189 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 40)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/40
`/scratch/stefan/7787277/working/3D/40' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497189.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497189.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497189/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497189 none CCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 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, 81, 81, 81, 81, 81, 81, 81, 81, 81, 71, 81, 54, 54, 27, 54, 13, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 81, 81, 81, 81, 81, 81, 81, 71, 71, 54, 27, 27, 1] 83
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])
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: REAL300025497189 none CCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 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: [5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 44, 50, 81, 81, 81, 81, 81, 5, 5, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 5, 5, 12, 44, 44, 81] 83
rigid atoms, others: [32, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 3, 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])
total number of confs: 239
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497189 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497189
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497189/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497189
Building REAL300025497190
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497190'
/scratch/stefan/7787277/working/building/REAL300025497190 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497190

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497190/0 /scratch/stefan/7787277/working/building/REAL300025497190 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 41)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/41
`/scratch/stefan/7787277/working/3D/41' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497190.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497190.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497190/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497190 none COCCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 136, 136, 136, 136, 136, 136, 136, 136, 136, 100, 136, 66, 66, 29, 66, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 196, 196, 136, 136, 136, 136, 136, 136, 136, 100, 100, 66, 29, 29, 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: 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: REAL300025497190 none COCCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 11, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 9, 9, 9, 34, 50, 136, 136, 136, 136, 136, 22, 22, 22, 11, 11, 8, 8, 1, 1, 1, 1, 2, 2, 2, 5, 5, 9, 34, 34, 136] 201
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 341
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497190 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497190
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497190/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497190
Building REAL300025497191
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497191'
/scratch/stefan/7787277/working/building/REAL300025497191 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497191

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497191/0 /scratch/stefan/7787277/working/building/REAL300025497191 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 42)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/42
`/scratch/stefan/7787277/working/3D/42' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497191.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497191.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497191/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497191 none CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [194, 194, 194, 194, 194, 194, 194, 194, 194, 193, 194, 148, 148, 65, 148, 13, 1, 1, 1, 1, 1, 1, 1, 194, 194, 194, 194, 194, 194, 194, 194, 194, 194, 193, 193, 148, 65, 65, 1] 194
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])
total number of confs: 706
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497191 none CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
194  conformations in input
total number of sets (complete confs): 194
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 16, 16, 16, 60, 116, 194, 194, 194, 194, 194, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 5, 5, 16, 60, 60, 194] 194
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 453
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497191 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497191
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497191/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497191
Building REAL300025497192
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497192'
/scratch/stefan/7787277/working/building/REAL300025497192 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497192

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497192/0 /scratch/stefan/7787277/working/building/REAL300025497192 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 43)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/43
`/scratch/stefan/7787277/working/3D/43' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C1CC1)

`REAL300025497192.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497192.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497192/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497192 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 5, 5, 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, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [73, 60, 46, 46, 24, 46, 12, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 73, 73, 73, 73, 73, 85, 85, 73, 73, 73, 60, 60, 46, 24, 24, 1, 73, 73, 73, 73, 85, 85, 85, 85, 85] 85
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: 320
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497192 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 5, 5, 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, 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
85  conformations in input
total number of sets (complete confs): 85
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 14, 27, 27, 27, 62, 69, 85, 85, 85, 85, 85, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 7, 7, 7, 14, 14, 27, 62, 62, 85, 7, 7, 7, 7, 1, 1, 1, 1, 1] 85
rigid atoms, others: [38, 39, 40, 41, 42, 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])
total number of confs: 279
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497192 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 5, 5, 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, 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
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, 5, 12, 12, 12, 39, 47, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 2, 2, 2, 5, 5, 12, 39, 39, 72, 1, 1, 1, 1, 7, 7, 7, 7, 7] 85
rigid atoms, others: [0, 1, 2, 35, 36, 37, 34, 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, 38, 39, 40, 41, 42])
total number of confs: 215
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497192 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497192
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497192/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497192
Building REAL300025497193
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497193'
/scratch/stefan/7787277/working/building/REAL300025497193 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497193

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497193/0 /scratch/stefan/7787277/working/building/REAL300025497193 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 44)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/44
`/scratch/stefan/7787277/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)CC(F)(F)CN1C(=O)C1CCC1)

`REAL300025497193.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497193.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497193/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497193 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 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, 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
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [64, 54, 44, 44, 23, 44, 11, 1, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64, 64, 64, 64, 64, 64, 82, 82, 82, 64, 64, 64, 54, 54, 44, 23, 23, 1, 64, 64, 64, 64, 82, 82, 82, 82, 82, 82, 82] 82
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: 305
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497193 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 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, 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
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 14, 28, 28, 28, 61, 67, 82, 82, 82, 82, 82, 5, 5, 5, 5, 5, 5, 1, 5, 1, 1, 1, 1, 5, 5, 5, 14, 14, 28, 61, 61, 82, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1] 82
rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 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])
total number of confs: 269
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497193 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 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, 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
82  conformations in input
total number of sets (complete confs): 82
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 12, 12, 12, 36, 41, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 2, 2, 2, 5, 5, 12, 36, 36, 64, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5] 82
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 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, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 192
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497193 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497193
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497193/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497193
Building REAL300025497194
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497194'
/scratch/stefan/7787277/working/building/REAL300025497194 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497194

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497194/0 /scratch/stefan/7787277/working/building/REAL300025497194 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 45)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/45
`/scratch/stefan/7787277/working/3D/45' -> `0.mol2'
Preparing input files

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

`REAL300025497194.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497194.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497194/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497194 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C(N)=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [35, 33, 25, 25, 18, 25, 11, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 36, 36, 35, 35, 35, 33, 33, 25, 18, 18, 1, 35, 35, 35, 35, 36, 36] 36
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])
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: REAL300025497194 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C(N)=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 7, 7, 6, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 4, 10, 10, 10, 22, 25, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 2, 2, 2, 4, 4, 10, 22, 22, 35, 1, 1, 1, 1, 7, 7] 36
rigid atoms, others: [0, 1, 2, 35, 36, 37, 34, 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, 38, 39])
total number of confs: 125
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497194 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497194
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497194/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497194
Building REAL300025497195
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497195'
/scratch/stefan/7787277/working/building/REAL300025497195 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497195

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497195/0 /scratch/stefan/7787277/working/building/REAL300025497195 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 46)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/46
`/scratch/stefan/7787277/working/3D/46' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497195.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497195.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497195/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497195 none C[C@@H]1C[C@H]1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
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, 8, 2, 8, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 35, 40, 69, 69, 69, 69, 69, 8, 8, 8, 8, 8, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 35, 35, 69] 91
rigid atoms, others: [33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 203
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497195 none C[C@@H]1C[C@H]1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
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, 70, 91, 69, 70, 69, 69, 69, 69, 69, 69, 56, 69, 45, 45, 26, 45, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 69, 69, 69, 69, 69, 69, 69, 56, 56, 45, 26, 26, 1] 91
rigid atoms, others: [45, 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])
total number of confs: 343
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497195 none C[C@@H]1C[C@H]1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
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, 1, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 16, 30, 30, 30, 65, 72, 91, 91, 91, 91, 91, 2, 2, 2, 1, 1, 8, 8, 8, 8, 8, 8, 8, 16, 16, 30, 65, 65, 91] 91
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 305
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497195 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497195
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497195/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497195
Building REAL300025497196
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497196'
/scratch/stefan/7787277/working/building/REAL300025497196 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497196

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497196/0 /scratch/stefan/7787277/working/building/REAL300025497196 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 47)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/47
`/scratch/stefan/7787277/working/3D/47' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(F)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497196.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497196.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497196/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497196 none CCC(F)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 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
125  conformations in input
total number of sets (complete confs): 125
using faster count positions algorithm for large data
unique positions, atoms: [125, 125, 111, 125, 111, 111, 111, 111, 111, 111, 111, 111, 97, 111, 68, 68, 30, 68, 13, 1, 1, 1, 1, 1, 1, 1, 125, 125, 125, 125, 125, 125, 111, 111, 111, 111, 111, 111, 111, 97, 97, 68, 30, 30, 1] 125
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: 484
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497196 none CCC(F)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 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
125  conformations in input
total number of sets (complete confs): 125
using faster count positions algorithm for large data
unique positions, atoms: [8, 6, 2, 6, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16, 16, 16, 50, 63, 111, 111, 111, 111, 111, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 2, 2, 2, 6, 6, 16, 50, 50, 111] 125
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 5, 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])
total number of confs: 322
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497196 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497196
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497196/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497196
Building REAL300025497197
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497197'
/scratch/stefan/7787277/working/building/REAL300025497197 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497197

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497197/0 /scratch/stefan/7787277/working/building/REAL300025497197 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 48)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/48
`/scratch/stefan/7787277/working/3D/48' -> `0.mol2'
Preparing input files

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

`REAL300025497197.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497197.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497197/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497197 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)CCCF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', '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', 'F', '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, 15, 15, 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, 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
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [95, 70, 49, 49, 22, 49, 13, 1, 1, 1, 1, 1, 1, 1, 95, 95, 95, 95, 95, 95, 95, 95, 95, 164, 175, 175, 95, 95, 95, 70, 70, 49, 22, 22, 1, 95, 95, 95, 95, 164, 164, 175, 175, 175, 175] 175
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: 803
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497197 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)CCCF NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', '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', 'F', '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, 15, 15, 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, 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
175  conformations in input
total number of sets (complete confs): 175
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 9, 9, 9, 33, 36, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 11, 24, 2, 2, 2, 5, 5, 9, 33, 33, 95, 1, 1, 1, 1, 8, 8, 13, 13, 22, 23] 175
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 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, 39, 40, 41, 42, 43, 44])
total number of confs: 322
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497197 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497197
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497197/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497197
Building REAL300025497198
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497198'
/scratch/stefan/7787277/working/building/REAL300025497198 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497198

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497198/0 /scratch/stefan/7787277/working/building/REAL300025497198 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 49)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/49
`/scratch/stefan/7787277/working/3D/49' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1C[C@@H]1C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497198.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497198.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497198/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497198 none C[C@H]1C[C@@H]1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 38, 44, 73, 73, 73, 73, 73, 7, 7, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 38, 38, 73] 94
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 36] set([0, 1, 2, 3, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497198 none C[C@H]1C[C@@H]1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [94, 94, 94, 94, 73, 94, 73, 73, 73, 73, 73, 73, 73, 73, 61, 73, 47, 47, 25, 47, 12, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 73, 73, 73, 73, 73, 73, 73, 61, 61, 47, 25, 25, 1] 94
rigid atoms, others: [45, 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])
total number of confs: 357
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497198 none C[C@H]1C[C@@H]1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
94  conformations in input
total number of sets (complete confs): 94
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 29, 29, 29, 70, 76, 94, 94, 94, 94, 94, 2, 2, 2, 1, 1, 7, 7, 7, 7, 7, 7, 7, 14, 14, 29, 70, 70, 94] 94
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 327
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497198 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497198
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497198/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497198
Building REAL300025497199
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497199'
/scratch/stefan/7787277/working/building/REAL300025497199 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497199

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497199/0 /scratch/stefan/7787277/working/building/REAL300025497199 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 50)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/50
`/scratch/stefan/7787277/working/3D/50' -> `0.mol2'
Preparing input files

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

`REAL300025497199.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497199.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497199/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497199 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)CO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', '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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [40, 36, 28, 28, 16, 28, 9, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 36, 36, 28, 16, 16, 1, 40, 40, 40, 40, 40, 40, 120] 120
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])
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: REAL300025497199 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)CO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', '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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 12, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 7, 7, 6, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
120  conformations in input
total number of sets (complete confs): 120
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 4, 9, 9, 9, 24, 26, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 2, 2, 2, 4, 4, 9, 24, 24, 40, 1, 1, 1, 1, 4, 4, 12] 120
rigid atoms, others: [0, 1, 2, 35, 36, 33, 34, 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, 37, 38, 39])
total number of confs: 149
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497199 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497199
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497199/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497199
Building REAL300025497200
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497200'
/scratch/stefan/7787277/working/building/REAL300025497200 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497200

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497200/0 /scratch/stefan/7787277/working/building/REAL300025497200 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 51)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/51
`/scratch/stefan/7787277/working/3D/51' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C1CCO1)

`REAL300025497200.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497200.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497200/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497200 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C1CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', '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', 'F', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 5, 5, 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, 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]
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, 147, 86, 86, 35, 86, 13, 1, 1, 1, 1, 1, 1, 1, 163, 163, 163, 163, 163, 163, 163, 163, 163, 163, 163, 163, 163, 163, 163, 147, 147, 86, 35, 35, 1, 163, 163, 163, 163, 163, 163, 163, 163, 163] 163
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: 618
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497200 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C1CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', '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', 'F', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 5, 5, 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, 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]
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: [6, 6, 6, 16, 36, 36, 36, 92, 117, 163, 163, 163, 163, 163, 6, 6, 6, 6, 6, 5, 1, 5, 1, 1, 1, 1, 6, 6, 6, 16, 16, 36, 92, 92, 163, 6, 6, 6, 6, 1, 1, 1, 1, 1] 163
rigid atoms, others: [39, 40, 41, 42, 43, 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])
total number of confs: 480
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497200 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C1CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', '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', 'F', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 5, 5, 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, 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]
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, 8, 24, 24, 24, 79, 107, 163, 163, 163, 163, 163, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 2, 2, 2, 8, 8, 24, 79, 79, 163, 1, 1, 1, 1, 6, 6, 6, 6, 6] 163
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 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, 39, 40, 41, 42, 43])
total number of confs: 462
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497200 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497200
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497200/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497200
Building REAL300025497201
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497201'
/scratch/stefan/7787277/working/building/REAL300025497201 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497201

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497201/0 /scratch/stefan/7787277/working/building/REAL300025497201 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 52)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/52
`/scratch/stefan/7787277/working/3D/52' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C1COC1)

`REAL300025497201.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497201.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497201/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497201 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C1COC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', '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', 'F', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 5, 12, 5, 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, 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
74  conformations in input
total number of sets (complete confs): 74
using faster count positions algorithm for large data
unique positions, atoms: [60, 49, 40, 40, 22, 40, 11, 1, 1, 1, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 60, 60, 60, 74, 74, 74, 60, 60, 60, 49, 49, 40, 22, 22, 1, 60, 60, 60, 60, 74, 74, 74, 74, 74] 74
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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497201 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C1COC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', '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', 'F', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 5, 12, 5, 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, 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
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, 16, 30, 30, 30, 58, 62, 74, 74, 74, 74, 74, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 6, 6, 6, 16, 16, 30, 58, 58, 74, 6, 6, 6, 6, 1, 1, 1, 1, 1] 74
rigid atoms, others: [39, 40, 41, 42, 43, 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])
total number of confs: 247
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497201 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C1COC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', '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', 'F', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 5, 12, 5, 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, 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
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, 5, 12, 12, 12, 34, 37, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 6, 6, 2, 2, 2, 5, 5, 12, 34, 34, 60, 1, 1, 1, 1, 6, 6, 6, 6, 6] 74
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 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, 39, 40, 41, 42, 43])
total number of confs: 182
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497201 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497201
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497201/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497201
Building REAL300025497202
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497202'
/scratch/stefan/7787277/working/building/REAL300025497202 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497202

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497202/0 /scratch/stefan/7787277/working/building/REAL300025497202 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 53)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/53
`/scratch/stefan/7787277/working/3D/53' -> `0.mol2'
Preparing input files

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

`REAL300025497202.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497202.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497202/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497202 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C=CCO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', '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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 1, 1, 5, 12, 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, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [162, 132, 96, 96, 33, 96, 13, 1, 1, 1, 1, 1, 1, 1, 162, 162, 162, 162, 162, 162, 162, 162, 162, 201, 201, 201, 162, 162, 162, 132, 132, 96, 33, 33, 1, 162, 162, 162, 162, 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])
total number of confs: 1353
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497202 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C=CCO NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.am', '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', 'F', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 1, 1, 5, 12, 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, 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]
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, 31, 59, 162, 162, 162, 162, 162, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 8, 29, 2, 2, 2, 4, 4, 7, 31, 31, 162, 1, 1, 1, 1, 8, 8, 29, 29, 87] 603
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 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, 39, 40, 41, 42, 43])
total number of confs: 496
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497202 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497202
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497202/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497202
Building REAL300025497203
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497203'
/scratch/stefan/7787277/working/building/REAL300025497203 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497203

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497203/0 /scratch/stefan/7787277/working/building/REAL300025497203 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 54)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/54
`/scratch/stefan/7787277/working/3D/54' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497203.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497203.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497203/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497203 none CCC=CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 180, 132, 130, 132, 130, 130, 130, 130, 130, 130, 96, 130, 59, 59, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 180, 180, 130, 130, 130, 130, 130, 130, 130, 96, 96, 59, 29, 29, 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: 827
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497203 none CCC=CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 25, 36, 130, 130, 130, 130, 130, 24, 24, 24, 24, 24, 10, 10, 1, 1, 1, 1, 2, 2, 2, 5, 5, 8, 25, 25, 130] 201
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 333
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497203 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497203
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497203/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497203
Building REAL300025497204
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497204'
/scratch/stefan/7787277/working/building/REAL300025497204 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497204

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497204/0 /scratch/stefan/7787277/working/building/REAL300025497204 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 55)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/55
`/scratch/stefan/7787277/working/3D/55' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497204.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497204.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497204/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497204 none C#CCCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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, 199, 133, 129, 133, 129, 129, 129, 129, 129, 129, 89, 129, 56, 56, 28, 56, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 199, 199, 129, 129, 129, 129, 129, 129, 129, 89, 89, 56, 28, 28, 1] 201
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: 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: REAL300025497204 none C#CCCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 10, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 35, 47, 129, 129, 129, 129, 129, 15, 15, 15, 10, 10, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 35, 35, 129] 201
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 5, 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: 336
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497204 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497204
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497204/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497204
Building REAL300025497205
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497205'
/scratch/stefan/7787277/working/building/REAL300025497205 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497205

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497205/0 /scratch/stefan/7787277/working/building/REAL300025497205 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 56)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/56
`/scratch/stefan/7787277/working/3D/56' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(O)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497205.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497205.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497205/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497205 none C=CC(O)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 19, 20, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 15, 15, 12, 15, 9, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 60, 19, 19, 19, 19, 19, 19, 19, 19, 19, 15, 12, 12, 1] 60
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: 127
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: REAL300025497205 none C=CC(O)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [1, 1, 5, 12, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 14, 14, 19, 19, 19, 19, 19, 6, 6, 6, 3, 9, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 14, 14, 19] 60
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 5, 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: 100
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497205 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497205
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497205/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497205
Building REAL300025497206
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497206'
/scratch/stefan/7787277/working/building/REAL300025497206 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497206

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497206/0 /scratch/stefan/7787277/working/building/REAL300025497206 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 57)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/57
`/scratch/stefan/7787277/working/3D/57' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497206.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497206.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497206/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497206 none CC(O)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 6]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
267  conformations in input
total number of sets (complete confs): 267
using faster count positions algorithm for large data
unique positions, atoms: [89, 86, 89, 86, 86, 86, 86, 86, 86, 86, 86, 80, 86, 64, 64, 29, 64, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 89, 267, 86, 86, 86, 86, 86, 86, 86, 80, 80, 64, 29, 29, 1] 267
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: 597
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: REAL300025497206 none CC(O)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 5, 12, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 6]
dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
267  conformations in input
total number of sets (complete confs): 267
using faster count positions algorithm for large data
unique positions, atoms: [4, 2, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 49, 60, 86, 86, 86, 86, 86, 4, 4, 4, 4, 12, 1, 1, 1, 1, 2, 2, 2, 6, 6, 14, 49, 49, 86] 267
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 282
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497206 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497206
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497206/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497206
Building REAL300025497207
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497207'
/scratch/stefan/7787277/working/building/REAL300025497207 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497207

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497207/0 /scratch/stefan/7787277/working/building/REAL300025497207 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 58)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/58
`/scratch/stefan/7787277/working/3D/58' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497207.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497207.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497207/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497207 none CC(=O)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [55, 52, 55, 52, 52, 52, 52, 52, 52, 52, 52, 49, 52, 36, 36, 21, 36, 12, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 52, 52, 52, 52, 52, 52, 52, 49, 49, 36, 21, 21, 1] 55
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])
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: REAL300025497207 none CC(=O)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 1, 11, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
55  conformations in input
total number of sets (complete confs): 55
using faster count positions algorithm for large data
unique positions, atoms: [6, 2, 6, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 32, 37, 52, 52, 52, 52, 52, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 5, 5, 14, 32, 32, 52] 55
rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29, 30, 31] set([0, 1, 2, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 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/7787277/working/building/REAL300025497207 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497207
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497207/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497207
Building REAL300025497208
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497208'
/scratch/stefan/7787277/working/building/REAL300025497208 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497208

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497208/0 /scratch/stefan/7787277/working/building/REAL300025497208 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 59)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/59
`/scratch/stefan/7787277/working/3D/59' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(F)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497208.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497208.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497208/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497208 none CC=C(F)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [111, 111, 105, 111, 104, 105, 104, 104, 104, 104, 104, 104, 86, 104, 67, 67, 31, 67, 13, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 104, 104, 104, 104, 104, 104, 104, 86, 86, 67, 31, 31, 1] 111
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: 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: REAL300025497208 none CC=C(F)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', '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']
dock atom type numbers: [5, 1, 1, 15, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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
111  conformations in input
total number of sets (complete confs): 111
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 3, 9, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 52, 64, 104, 104, 104, 104, 104, 9, 9, 9, 9, 1, 1, 1, 1, 2, 2, 2, 6, 6, 14, 52, 52, 104] 111
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 299
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497208 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497208
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497208/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497208
Building REAL300025497209
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497209'
/scratch/stefan/7787277/working/building/REAL300025497209 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497209

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497209/0 /scratch/stefan/7787277/working/building/REAL300025497209 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 60)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/60
`/scratch/stefan/7787277/working/3D/60' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CO)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497209.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497209.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497209/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497209 none CC(CO)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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
531  conformations in input
total number of sets (complete confs): 531
using faster count positions algorithm for large data
unique positions, atoms: [177, 160, 177, 177, 157, 160, 157, 157, 157, 157, 157, 157, 135, 157, 86, 86, 41, 86, 13, 1, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 177, 177, 531, 157, 157, 157, 157, 157, 157, 157, 135, 135, 86, 41, 41, 1] 531
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: 1248
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: REAL300025497209 none CC(CO)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 5, 12, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 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
531  conformations in input
total number of sets (complete confs): 531
using faster count positions algorithm for large data
unique positions, atoms: [8, 3, 8, 20, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 47, 60, 157, 157, 157, 157, 157, 8, 8, 8, 8, 20, 20, 60, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 47, 47, 157] 531
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 477
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497209 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497209
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497209/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497209
Building REAL300025497210
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497210'
/scratch/stefan/7787277/working/building/REAL300025497210 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497210

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497210/0 /scratch/stefan/7787277/working/building/REAL300025497210 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 61)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/61
`/scratch/stefan/7787277/working/3D/61' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C1=CCC1)

`REAL300025497210.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497210.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497210/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497210 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 46, 39, 39, 24, 39, 13, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 46, 46, 39, 24, 24, 1, 52, 52, 52, 52, 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])
total number of confs: 175
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497210 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [8, 8, 8, 15, 23, 23, 23, 42, 46, 52, 52, 52, 52, 52, 8, 8, 8, 8, 8, 6, 1, 6, 1, 1, 1, 1, 8, 8, 8, 15, 15, 23, 42, 42, 52, 8, 8, 8, 8, 1, 1, 1, 1, 1] 52
rigid atoms, others: [39, 40, 41, 42, 43, 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])
total number of confs: 182
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497210 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 5, 10, 10, 10, 31, 35, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 2, 2, 2, 5, 5, 10, 31, 31, 52, 1, 1, 1, 1, 8, 8, 8, 8, 8] 52
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 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, 39, 40, 41, 42, 43])
total number of confs: 170
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497210 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497210
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497210/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497210
Building REAL300025497211
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497211'
/scratch/stefan/7787277/working/building/REAL300025497211 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497211

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497211/0 /scratch/stefan/7787277/working/building/REAL300025497211 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 62)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/62
`/scratch/stefan/7787277/working/3D/62' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CF)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497211.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497211.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497211/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497211 none CC(CF)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 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
133  conformations in input
total number of sets (complete confs): 133
using faster count positions algorithm for large data
unique positions, atoms: [133, 126, 133, 133, 124, 126, 124, 124, 124, 124, 124, 124, 111, 124, 65, 65, 35, 65, 13, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 133, 133, 133, 124, 124, 124, 124, 124, 124, 124, 111, 111, 65, 35, 35, 1] 133
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: 539
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497211 none CC(CF)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 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
133  conformations in input
total number of sets (complete confs): 133
using faster count positions algorithm for large data
unique positions, atoms: [6, 3, 6, 14, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 42, 49, 124, 124, 124, 124, 124, 6, 6, 6, 6, 14, 14, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 42, 42, 124] 133
rigid atoms, others: [32, 33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 5, 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])
total number of confs: 335
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497211 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497211
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497211/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497211
Building REAL300025497212
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497212'
/scratch/stefan/7787277/working/building/REAL300025497212 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497212

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497212/0 /scratch/stefan/7787277/working/building/REAL300025497212 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 63)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/63
`/scratch/stefan/7787277/working/3D/63' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497212.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497212.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497212/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497212 none CC=CC(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 54, 54, 54, 54, 54, 54, 54, 54, 54, 49, 54, 38, 38, 21, 38, 13, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 54, 54, 54, 54, 54, 54, 54, 49, 49, 38, 21, 21, 1] 56
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: 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: REAL300025497212 none CC=CC(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 33, 35, 54, 54, 54, 54, 54, 7, 7, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 33, 33, 54] 56
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 175
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497212 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497212
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497212/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497212
Building REAL300025497213
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497213'
/scratch/stefan/7787277/working/building/REAL300025497213 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497213

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497213/0 /scratch/stefan/7787277/working/building/REAL300025497213 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 64)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/64
`/scratch/stefan/7787277/working/3D/64' -> `0.mol2'
Preparing input files

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

`REAL300025497213.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497213.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497213/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497213 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [94, 78, 44, 44, 23, 44, 12, 1, 1, 1, 1, 1, 1, 1, 94, 94, 94, 94, 94, 94, 94, 95, 95, 135, 135, 135, 94, 94, 94, 78, 78, 44, 23, 23, 1, 94, 94, 94, 94, 135, 135, 135, 135] 135
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: 535
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497213 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 5, 10, 10, 10, 34, 35, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 41, 2, 2, 2, 5, 5, 10, 34, 34, 94, 1, 1, 1, 1, 11, 11, 41, 41] 135
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 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, 39, 40, 41, 42])
total number of confs: 355
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497213 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497213
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497213/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497213
Building REAL300025497214
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497214'
/scratch/stefan/7787277/working/building/REAL300025497214 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497214

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497214/0 /scratch/stefan/7787277/working/building/REAL300025497214 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 65)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/65
`/scratch/stefan/7787277/working/3D/65' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NC(=O)NN2)CC(F)(F)CN1C(=O)CN=[N+]=[N-])

`REAL300025497214.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497214.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497214/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497214 none CC1(CNC(=O)CSC2=NC(=O)NN2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 1, 11, 8, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [87, 63, 45, 45, 25, 45, 9, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87, 87, 87, 87, 87, 87, 160, 201, 201, 87, 87, 87, 63, 63, 45, 25, 25, 1, 1, 87, 87, 87, 87, 160, 160] 201
rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41])
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: REAL300025497214 none CC1(CNC(=O)CSC2=NC(=O)NN2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 1, 11, 8, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 13, 13, 13, 35, 62, 87, 87, 87, 87, 87, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 48, 48, 2, 2, 2, 8, 8, 13, 35, 35, 87, 87, 1, 1, 1, 1, 12, 12] 201
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 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, 40, 41])
total number of confs: 299
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497214 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497214/1 /scratch/stefan/7787277/working/building/REAL300025497214 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 66)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/66
`/scratch/stefan/7787277/working/3D/66' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NC(=O)[N-]N2)CC(F)(F)CN1C(=O)CN=[N+]=[N-])

`REAL300025497214.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497214.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497214/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497214 none CC1(CNC(=O)CSC2=NC(=O)[N-]N2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 1, 11, 8, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [43, 37, 26, 26, 16, 26, 11, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 76, 110, 110, 43, 43, 43, 37, 37, 26, 16, 16, 1, 43, 43, 43, 43, 76, 76] 110
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])
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: REAL300025497214 none CC1(CNC(=O)CSC2=NC(=O)[N-]N2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 1, 11, 8, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 8, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 6, 6, 6, 19, 20, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 43, 43, 2, 2, 2, 3, 3, 6, 19, 19, 43, 1, 1, 1, 1, 12, 12] 110
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 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, 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/7787277/working/building/REAL300025497214 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497214
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497214/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497214/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497214
Building REAL300025497215
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497215'
/scratch/stefan/7787277/working/building/REAL300025497215 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497215

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497215/0 /scratch/stefan/7787277/working/building/REAL300025497215 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 67)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/67
`/scratch/stefan/7787277/working/3D/67' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](O)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497215.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497215.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497215/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497215 none C[C@H](O)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  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: [55, 53, 55, 55, 53, 53, 53, 53, 53, 53, 53, 53, 47, 53, 39, 39, 21, 39, 12, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 165, 53, 53, 53, 53, 53, 53, 53, 47, 47, 39, 21, 21, 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: 366
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: REAL300025497215 none C[C@H](O)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
165  conformations in input
total number of sets (complete confs): 165
using faster count positions algorithm for large data
unique positions, atoms: [4, 2, 4, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 33, 36, 53, 53, 53, 53, 53, 4, 4, 4, 12, 1, 1, 1, 1, 2, 2, 2, 4, 4, 11, 33, 33, 53] 165
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 188
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497215 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497215
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497215/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497215
Building REAL300025497216
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497216'
/scratch/stefan/7787277/working/building/REAL300025497216 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497216

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497216/0 /scratch/stefan/7787277/working/building/REAL300025497216 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 68)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/68
`/scratch/stefan/7787277/working/3D/68' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CON=CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497216.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497216.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497216/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497216 none CON=CC(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 165, 150, 165, 150, 150, 150, 150, 150, 150, 111, 150, 64, 64, 30, 64, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 150, 150, 150, 150, 150, 150, 150, 111, 111, 64, 30, 30, 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: 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: REAL300025497216 none CON=CC(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 12, 8, 1, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [18, 10, 10, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 13, 39, 57, 150, 150, 150, 150, 150, 18, 18, 18, 10, 1, 1, 1, 1, 2, 2, 2, 6, 6, 13, 39, 39, 150] 201
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 353
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497216 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497216
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497216/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497216
Building REAL300025497217
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497217'
/scratch/stefan/7787277/working/building/REAL300025497217 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497217

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497217/0 /scratch/stefan/7787277/working/building/REAL300025497217 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 69)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/69
`/scratch/stefan/7787277/working/3D/69' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#C[C@H]1C[C@H]1C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497217.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497217.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497217/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497217 none C#C[C@H]1C[C@H]1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 3, 9, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 60, 94, 179, 179, 179, 179, 179, 9, 9, 9, 1, 1, 1, 1, 2, 2, 2, 7, 7, 19, 60, 60, 179] 201
rigid atoms, others: [32, 33, 34, 35, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 8, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 438
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497217 none C#C[C@H]1C[C@H]1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 192, 201, 179, 192, 179, 179, 179, 179, 179, 179, 154, 179, 91, 91, 31, 91, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 179, 179, 179, 179, 179, 179, 179, 154, 154, 91, 31, 31, 1] 201
rigid atoms, others: [44, 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])
total number of confs: 762
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497217 none C#C[C@H]1C[C@H]1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 20, 35, 35, 35, 95, 132, 201, 201, 201, 201, 201, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 20, 20, 35, 95, 95, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 547
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497217 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497217
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497217/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497217
Building REAL300025497218
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497218'
/scratch/stefan/7787277/working/building/REAL300025497218 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497218

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497218/0 /scratch/stefan/7787277/working/building/REAL300025497218 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 70)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/70
`/scratch/stefan/7787277/working/3D/70' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(F)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497218.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497218.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497218/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497218 none COC(F)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 12, 5, 15, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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
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, 7, 8, 7, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 1] 8
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: 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: REAL300025497218 none COC(F)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 12, 5, 15, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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
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, 1, 1, 3, 4, 4, 4, 6, 6, 8, 8, 8, 8, 8, 4, 4, 4, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 4, 6, 6, 8] 8
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 44
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497218 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497218
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497218/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497218
Building REAL300025497219
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497219'
/scratch/stefan/7787277/working/building/REAL300025497219 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497219

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497219/0 /scratch/stefan/7787277/working/building/REAL300025497219 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 71)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/71
`/scratch/stefan/7787277/working/3D/71' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497219.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497219.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497219/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497219 none C[C@@H]1C[C@H]1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
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, 8, 2, 8, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 35, 40, 69, 69, 69, 69, 69, 8, 8, 8, 8, 8, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 35, 35, 69] 91
rigid atoms, others: [33, 34, 35, 36, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 203
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497219 none C[C@@H]1C[C@H]1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
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, 70, 91, 69, 70, 69, 69, 69, 69, 69, 69, 56, 69, 45, 45, 26, 45, 13, 1, 1, 1, 1, 1, 1, 1, 91, 91, 91, 91, 91, 69, 69, 69, 69, 69, 69, 69, 56, 56, 45, 26, 26, 1] 91
rigid atoms, others: [45, 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])
total number of confs: 343
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497219 none C[C@@H]1C[C@H]1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
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, 1, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 16, 30, 30, 30, 65, 72, 91, 91, 91, 91, 91, 2, 2, 2, 1, 1, 8, 8, 8, 8, 8, 8, 8, 16, 16, 30, 65, 65, 91] 91
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 305
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497219 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497219
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497219/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497219
Building REAL300025497220
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497220'
/scratch/stefan/7787277/working/building/REAL300025497220 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497220

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497220/0 /scratch/stefan/7787277/working/building/REAL300025497220 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 72)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/72
`/scratch/stefan/7787277/working/3D/72' -> `0.mol2'
Preparing input files

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

`REAL300025497220.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497220.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497220/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497220 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 7, 12, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [41, 33, 24, 24, 17, 24, 12, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 44, 44, 44, 44, 41, 41, 41, 33, 33, 24, 17, 17, 1, 41, 41, 41, 41, 132, 44, 44] 132
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])
total number of confs: 293
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: REAL300025497220 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 7, 12, 5, 15, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
132  conformations in input
total number of sets (complete confs): 132
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 8, 8, 8, 23, 23, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 14, 2, 2, 2, 3, 3, 8, 23, 23, 41, 1, 1, 1, 1, 21, 14, 14] 132
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 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, 40, 41, 42])
total number of confs: 201
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497220 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497220
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497220/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497220
Building REAL300025497221
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497221'
/scratch/stefan/7787277/working/building/REAL300025497221 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497221

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497221/0 /scratch/stefan/7787277/working/building/REAL300025497221 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 73)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/73
`/scratch/stefan/7787277/working/3D/73' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497221.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497221.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497221/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497221 none C=C(C)CC(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 122, 121, 122, 121, 121, 121, 121, 121, 121, 97, 121, 60, 60, 26, 60, 13, 1, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164, 164, 164, 164, 121, 121, 121, 121, 121, 121, 121, 97, 97, 60, 26, 26, 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: 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: REAL300025497221 none C=C(C)CC(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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: [28, 12, 28, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 41, 42, 121, 121, 121, 121, 121, 28, 28, 28, 28, 28, 12, 12, 1, 1, 1, 1, 2, 2, 2, 3, 3, 9, 41, 41, 121] 164
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 345
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497221 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497221
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497221/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497221
Building REAL300025497222
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497222'
/scratch/stefan/7787277/working/building/REAL300025497222 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497222

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497222/0 /scratch/stefan/7787277/working/building/REAL300025497222 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 74)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/74
`/scratch/stefan/7787277/working/3D/74' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497222.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497222.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497222/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497222 none C=CCC(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [159, 159, 107, 107, 107, 107, 107, 107, 107, 107, 107, 86, 107, 50, 50, 25, 50, 13, 1, 1, 1, 1, 1, 1, 1, 159, 159, 159, 159, 159, 107, 107, 107, 107, 107, 107, 107, 86, 86, 50, 25, 25, 1] 159
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: 717
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497222 none C=CCC(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
159  conformations in input
total number of sets (complete confs): 159
using faster count positions algorithm for large data
unique positions, atoms: [31, 11, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 10, 41, 41, 107, 107, 107, 107, 107, 31, 31, 31, 11, 11, 1, 1, 1, 1, 2, 2, 2, 3, 3, 10, 41, 41, 107] 159
rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 331
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497222 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497222
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497222/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497222
Building REAL300025497223
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497223'
/scratch/stefan/7787277/working/building/REAL300025497223 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497223

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497223/0 /scratch/stefan/7787277/working/building/REAL300025497223 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 75)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/75
`/scratch/stefan/7787277/working/3D/75' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497223.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497223.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497223/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497223 none C[NH+](C)CC(=O)N1CC(F)(F)CC1(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', 'F', '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, 9, 6, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 16, 16, 11, 16, 8, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 16, 11, 11, 1] 17
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: 50
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497223 none C[NH+](C)CC(=O)N1CC(F)(F)CC1(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', 'F', '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, 9, 6, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 14, 14, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 4, 4, 6, 14, 14, 17] 17
rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 37] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 81
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497223 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497223/1 /scratch/stefan/7787277/working/building/REAL300025497223 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 76)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/76
`/scratch/stefan/7787277/working/3D/76' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497223.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497223.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497223/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497223 none CN(C)CC(=O)N1CC(F)(F)CC1(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', 'F', '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, 10, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
66  conformations in input
total number of sets (complete confs): 66
using faster count positions algorithm for large data
unique positions, atoms: [66, 66, 66, 49, 49, 49, 49, 49, 49, 49, 49, 49, 40, 49, 26, 26, 17, 26, 12, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 49, 49, 49, 49, 49, 49, 49, 40, 40, 26, 17, 17, 1] 66
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: 284
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497223 none CN(C)CC(=O)N1CC(F)(F)CC1(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', 'F', '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, 10, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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: [15, 9, 15, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 24, 24, 49, 49, 49, 49, 49, 15, 15, 15, 15, 15, 15, 9, 9, 1, 1, 1, 1, 2, 2, 2, 3, 3, 8, 24, 24, 49] 66
rigid atoms, others: [34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 12, 13, 14, 36] 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, 38, 39, 40, 41, 42, 43, 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/7787277/working/building/REAL300025497223 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497223
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497223/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497223/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497223
Building REAL300025497224
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497224'
/scratch/stefan/7787277/working/building/REAL300025497224 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497224

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497224/0 /scratch/stefan/7787277/working/building/REAL300025497224 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 77)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/77
`/scratch/stefan/7787277/working/3D/77' -> `0.mol2'
Preparing input files

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

`REAL300025497224.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497224.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497224/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497224 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [51, 45, 34, 34, 18, 34, 11, 1, 1, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51, 58, 58, 51, 51, 51, 45, 45, 34, 18, 18, 1, 51, 51, 51, 51, 58, 58] 58
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])
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: REAL300025497224 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
58  conformations in input
total number of sets (complete confs): 58
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 9, 9, 9, 29, 30, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 2, 2, 2, 3, 3, 9, 29, 29, 51, 1, 1, 1, 1, 7, 7] 58
rigid atoms, others: [0, 1, 2, 35, 36, 37, 34, 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, 38, 39])
total number of confs: 165
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497224 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497224
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497224/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497224
Building REAL300025497225
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497225'
/scratch/stefan/7787277/working/building/REAL300025497225 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497225

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497225/0 /scratch/stefan/7787277/working/building/REAL300025497225 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 78)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/78
`/scratch/stefan/7787277/working/3D/78' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=O)C1CC1F)

`REAL300025497225.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497225.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497225/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497225 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [56, 48, 39, 39, 22, 39, 12, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 56, 56, 57, 57, 59, 59, 59, 56, 56, 56, 48, 48, 39, 22, 22, 1, 56, 56, 56, 56, 59, 59, 59, 59] 59
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: 213
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497225 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 12, 22, 22, 22, 45, 47, 59, 59, 59, 59, 59, 7, 7, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 7, 7, 7, 12, 12, 22, 45, 45, 59, 7, 7, 7, 7, 1, 1, 1, 1] 59
rigid atoms, others: [39, 40, 41, 42, 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])
total number of confs: 200
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497225 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 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]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
59  conformations in input
total number of sets (complete confs): 59
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 4, 11, 11, 11, 34, 36, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 7, 2, 2, 2, 4, 4, 11, 34, 34, 56, 1, 1, 1, 1, 7, 7, 7, 7] 59
rigid atoms, others: [0, 1, 2, 35, 36, 37, 38, 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, 39, 40, 41, 42])
total number of confs: 180
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497225 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497225
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497225/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497225
Building REAL300025497226
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497226'
/scratch/stefan/7787277/working/building/REAL300025497226 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497226

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497226/0 /scratch/stefan/7787277/working/building/REAL300025497226 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 79)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/79
`/scratch/stefan/7787277/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)CC(F)(F)CN1C(=O)CCF)

`REAL300025497226.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497226.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497226/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497226 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 5, 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, 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
107  conformations in input
total number of sets (complete confs): 107
using faster count positions algorithm for large data
unique positions, atoms: [90, 78, 54, 54, 29, 54, 13, 1, 1, 1, 1, 1, 1, 1, 90, 90, 90, 90, 90, 90, 90, 90, 90, 107, 107, 90, 90, 90, 78, 78, 54, 29, 29, 1, 90, 90, 90, 90, 107, 107, 107, 107] 107
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: 436
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497226 none CC1(CNC(=O)CSC2=NNC(=O)[N-]2)CC(F)(F)CN1C(=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', 'F', 'F', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 5, 8, 1, 11, 5, 5, 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, 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
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, 5, 14, 14, 14, 46, 51, 90, 90, 90, 90, 90, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 10, 2, 2, 2, 5, 5, 14, 46, 46, 90, 1, 1, 1, 1, 7, 7, 10, 10] 107
rigid atoms, others: [0, 1, 2, 35, 36, 37, 34, 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, 38, 39, 40, 41])
total number of confs: 279
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497226 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497226
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497226/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497226
Building REAL300025497227
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497227'
/scratch/stefan/7787277/working/building/REAL300025497227 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497227

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497227/0 /scratch/stefan/7787277/working/building/REAL300025497227 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 80)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/80
`/scratch/stefan/7787277/working/3D/80' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CO[C@H](C)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497227.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497227.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497227/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497227 none CO[C@H](C)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 16, 17, 17, 16, 16, 16, 16, 16, 16, 16, 16, 15, 16, 14, 14, 11, 14, 8, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 16, 16, 16, 16, 16, 16, 16, 15, 15, 14, 11, 11, 1] 17
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: 53
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497227 none CO[C@H](C)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 12, 5, 7, 5, 1, 11, 8, 5, 5, 15, 15, 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, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [5, 3, 2, 3, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 12, 12, 16, 16, 16, 16, 16, 5, 5, 5, 3, 3, 3, 1, 1, 1, 1, 2, 2, 2, 3, 3, 8, 12, 12, 16] 17
rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 68
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497227 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497227
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497227/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497227
Building REAL300025497228
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497228'
/scratch/stefan/7787277/working/building/REAL300025497228 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497228

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497228/0 /scratch/stefan/7787277/working/building/REAL300025497228 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 81)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/81
`/scratch/stefan/7787277/working/3D/81' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](O)C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497228.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497228.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497228/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497228 none C[C@@H](O)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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, 86, 89, 89, 86, 86, 86, 86, 86, 86, 86, 86, 80, 86, 64, 64, 29, 64, 13, 1, 1, 1, 1, 1, 1, 1, 89, 89, 89, 267, 86, 86, 86, 86, 86, 86, 86, 80, 80, 64, 29, 29, 1] 267
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: 597
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: REAL300025497228 none C[C@@H](O)C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 5, 7, 12, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 6, 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: [4, 2, 4, 4, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 49, 60, 86, 86, 86, 86, 86, 4, 4, 4, 12, 1, 1, 1, 1, 2, 2, 2, 6, 6, 14, 49, 49, 86] 267
rigid atoms, others: [32, 33, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 30, 31] set([0, 1, 2, 3, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 282
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497228 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497228
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497228/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497228
Building REAL300025497229
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497229'
/scratch/stefan/7787277/working/building/REAL300025497229 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497229

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497229/0 /scratch/stefan/7787277/working/building/REAL300025497229 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 82)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/82
`/scratch/stefan/7787277/working/3D/82' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C1CC1C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497229.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497229.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497229/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497229 none C=C1CC1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 42, 48, 81, 81, 81, 81, 81, 7, 7, 7, 7, 7, 1, 1, 1, 1, 2, 2, 2, 5, 5, 11, 42, 42, 81] 93
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 5, 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: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497229 none C=C1CC1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [93, 93, 93, 82, 81, 82, 81, 81, 81, 81, 81, 81, 67, 81, 53, 53, 26, 53, 13, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93, 93, 81, 81, 81, 81, 81, 81, 81, 67, 67, 53, 26, 26, 1] 93
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: 341
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497229 none C=C1CC1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
93  conformations in input
total number of sets (complete confs): 93
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 15, 29, 29, 29, 69, 74, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 15, 15, 29, 69, 69, 93] 93
rigid atoms, others: [0, 1, 2, 3, 4, 26, 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, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 315
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497229 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497229
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497229/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497229
Building REAL300025497230
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497230'
/scratch/stefan/7787277/working/building/REAL300025497230 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497230

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497230/0 /scratch/stefan/7787277/working/building/REAL300025497230 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 83)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/83
`/scratch/stefan/7787277/working/3D/83' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC1C(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497230.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497230.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497230/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497230 none CC1=CC1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 36, 42, 69, 69, 69, 69, 69, 8, 8, 8, 8, 8, 1, 1, 1, 1, 2, 2, 2, 4, 4, 9, 36, 36, 69] 86
rigid atoms, others: [32, 33, 34, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 5, 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: 210
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497230 none CC1=CC1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [86, 86, 86, 69, 69, 69, 69, 69, 69, 69, 69, 69, 60, 69, 49, 49, 27, 49, 13, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 69, 69, 69, 69, 69, 69, 69, 60, 60, 49, 27, 27, 1] 86
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: 311
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497230 none CC1=CC1C(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 5, 15, 15, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 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
86  conformations in input
total number of sets (complete confs): 86
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 16, 29, 29, 29, 66, 71, 86, 86, 86, 86, 86, 2, 2, 2, 1, 1, 8, 8, 8, 8, 8, 8, 8, 16, 16, 29, 66, 66, 86] 86
rigid atoms, others: [0, 1, 2, 3, 4, 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, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 304
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497230 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497230
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497230/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497230
Building REAL300025497231
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497231'
/scratch/stefan/7787277/working/building/REAL300025497231 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497231

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497231/0 /scratch/stefan/7787277/working/building/REAL300025497231 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 84)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/84
`/scratch/stefan/7787277/working/3D/84' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(=O)N1CC(F)(F)CC1(C)CNC(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497231.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497231.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497231/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497231 none C=CC(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 50, 40, 40, 21, 40, 12, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 40, 21, 21, 1] 50
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])
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: REAL300025497231 none C=CC(=O)N1CC(F)(F)CC1(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', 'F', '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']
dock atom type numbers: [1, 1, 1, 11, 8, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 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
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 10, 10, 10, 31, 35, 50, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 4, 4, 10, 31, 31, 50] 50
rigid atoms, others: [2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 27, 28, 29, 30] set([0, 1, 3, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 163
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497231 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497231
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497231/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497231
Building REAL300025497232
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497232'
/scratch/stefan/7787277/working/building/REAL300025497232 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497232

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497232/0 /scratch/stefan/7787277/working/building/REAL300025497232 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 85)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/85
`/scratch/stefan/7787277/working/3D/85' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CF)C(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497232.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497232.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497232/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497232 none CC(CF)C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 15, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 139, 201, 201, 139, 139, 86, 47, 47, 47, 47, 47, 47, 47, 47, 47, 34, 47, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 139, 86, 86, 47, 47, 47, 47, 47, 47, 47, 34, 34, 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: 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: REAL300025497232 none CC(CF)C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.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, 15, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 15, 48, 54, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 47, 47, 47, 47, 47, 48, 48, 48, 48, 54, 54, 15, 4, 4, 2, 2, 2, 1, 1, 1, 1, 5, 5, 47] 201
rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 39] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44])
total number of confs: 283
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497232 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497232
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497232/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497232
Building REAL300025497233
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497233'
/scratch/stefan/7787277/working/building/REAL300025497233 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497233

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497233/0 /scratch/stefan/7787277/working/building/REAL300025497233 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 86)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/86
`/scratch/stefan/7787277/working/3D/86' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CC(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497233.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497233.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497233/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497233 none C=C(C)CC(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 15, 15, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 127, 127, 127, 117, 77, 77, 77, 77, 77, 77, 77, 77, 71, 32, 71, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 127, 117, 117, 77, 77, 77, 77, 77, 77, 77, 32, 32, 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: 861
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497233 none C=C(C)CC(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', '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, 15, 15, 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]
dock color type numbers: [7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 41, 57, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 15, 77, 77, 77, 77, 77, 57, 57, 57, 57, 57, 41, 41, 7, 4, 4, 2, 2, 2, 1, 1, 1, 1, 7, 7, 77] 201
rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45])
total number of confs: 314
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497233 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497233
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497233/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497233
Building REAL300025497234
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497234'
/scratch/stefan/7787277/working/building/REAL300025497234 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497234

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497234/0 /scratch/stefan/7787277/working/building/REAL300025497234 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 87)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/87
`/scratch/stefan/7787277/working/3D/87' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=CC(=O)NCC1(C)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497234.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497234.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497234/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497234 none CC=CC(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 162, 162, 162, 151, 99, 99, 99, 99, 99, 99, 99, 99, 90, 32, 90, 13, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 162, 151, 151, 99, 99, 99, 99, 99, 99, 99, 32, 32, 1] 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])
total number of confs: 766
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497234 none CC=CC(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 7, 6, 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]
0  hydrogens 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, 9, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 22, 99, 99, 99, 99, 99, 29, 29, 29, 29, 29, 9, 5, 5, 2, 2, 2, 1, 1, 1, 1, 9, 9, 99] 201
rigid atoms, others: [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, 34, 35, 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
/scratch/stefan/7787277/working/building/REAL300025497234 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497234
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497234/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497234
Building REAL300025497235
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497235'
/scratch/stefan/7787277/working/building/REAL300025497235 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497235

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497235/0 /scratch/stefan/7787277/working/building/REAL300025497235 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 88)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/88
`/scratch/stefan/7787277/working/3D/88' -> `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)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497235.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497235.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497235/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497235 none C[C@@H]1C[C@H]1C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 7, 40, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 14, 74, 74, 74, 74, 74, 40, 40, 40, 40, 40, 7, 4, 4, 2, 2, 2, 1, 1, 1, 1, 7, 7, 74] 201
rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45])
total number of confs: 210
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497235 none C[C@@H]1C[C@H]1C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 104, 74, 74, 74, 74, 74, 74, 74, 74, 68, 32, 68, 12, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 115, 104, 104, 74, 74, 74, 74, 74, 74, 74, 32, 32, 1] 201
rigid atoms, others: [45, 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])
total number of confs: 724
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497235 none C[C@@H]1C[C@H]1C(=O)NCC1(C)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 5, 15, 15, 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, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 28, 40, 40, 40, 40, 40, 40, 40, 40, 47, 47, 85, 132, 201, 201, 201, 201, 201, 2, 2, 2, 1, 1, 12, 28, 28, 40, 40, 40, 40, 40, 40, 40, 85, 85, 201] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 567
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497235 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497235
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497235/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497235
Building REAL300025497236
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497236'
/scratch/stefan/7787277/working/building/REAL300025497236 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497236

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497236/0 /scratch/stefan/7787277/working/building/REAL300025497236 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 89)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/89
`/scratch/stefan/7787277/working/3D/89' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)[C@H](O)CF)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497236.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497236.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497236/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497236 none CC1(CNC(=O)[C@H](O)CF)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', '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, 7, 12, 5, 15, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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]
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: [45, 45, 45, 80, 137, 137, 137, 201, 201, 201, 201, 45, 45, 45, 45, 45, 45, 35, 45, 13, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 80, 80, 137, 603, 201, 201, 45, 45, 45, 45, 35, 35, 1] 603
rigid atoms, others: [42, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 1459
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497236 none CC1(CNC(=O)[C@H](O)CF)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', '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, 7, 12, 5, 15, 5, 5, 15, 15, 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, 6]
dock color type numbers: [7, 7, 7, 4, 7, 6, 7, 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]
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, 13, 13, 13, 38, 38, 38, 43, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 45, 45, 45, 45, 45, 2, 2, 2, 4, 4, 13, 114, 43, 43, 1, 1, 1, 1, 5, 5, 45] 603
rigid atoms, others: [0, 1, 2, 36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17] set([3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42])
total number of confs: 357
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497236 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497236
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497236/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497236
Building REAL300025497237
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497237'
/scratch/stefan/7787277/working/building/REAL300025497237 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497237

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497237/0 /scratch/stefan/7787277/working/building/REAL300025497237 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 90)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/90
`/scratch/stefan/7787277/working/3D/90' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CNC(=O)C2(O)CC2)CC(F)(F)CN1C(=O)CSC1=NNC(=O)[N-]1)

`REAL300025497237.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497237.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497237/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497237 none CC1(CNC(=O)C2(O)CC2)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 5, 5, 15, 15, 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, 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]
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: [64, 37, 9, 9, 1, 9, 1, 1, 1, 1, 64, 64, 64, 64, 64, 64, 64, 64, 64, 91, 135, 201, 201, 201, 201, 201, 64, 64, 64, 37, 37, 9, 6, 1, 1, 1, 1, 64, 64, 64, 64, 91, 91, 201] 603
rigid atoms, others: [33, 34, 35, 4, 6, 7, 8, 9, 36] 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, 31, 32, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 539
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497237 none CC1(CNC(=O)C2(O)CC2)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 5, 5, 15, 15, 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, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [73, 73, 73, 127, 179, 179, 179, 201, 201, 201, 73, 73, 73, 73, 73, 73, 43, 73, 13, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 127, 127, 179, 603, 201, 201, 201, 201, 73, 73, 73, 73, 43, 43, 1] 603
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: 1371
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497237 none CC1(CNC(=O)C2(O)CC2)CC(F)(F)CN1C(=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', 'F', 'F', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', '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, 5, 5, 5, 15, 15, 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, 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]
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, 20, 20, 20, 64, 64, 64, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 15, 73, 73, 73, 73, 73, 2, 2, 2, 6, 6, 20, 192, 64, 64, 64, 64, 1, 1, 1, 1, 7, 7, 73] 603
rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16] set([3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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
/scratch/stefan/7787277/working/building/REAL300025497237 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497237
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497237/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497237
Building REAL300025497238
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497238'
/scratch/stefan/7787277/working/building/REAL300025497238 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497238

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497238/0 /scratch/stefan/7787277/working/building/REAL300025497238 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 91)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/91
`/scratch/stefan/7787277/working/3D/91' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497238.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497238.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497238/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497238 none CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 136, 136, 136, 107, 107, 107, 107, 107, 93, 40, 93, 13, 1, 1, 1, 1, 1, 1, 1, 107, 201, 201, 201, 201, 201, 136, 107, 107, 107, 107, 107, 40, 40, 1, 107, 107] 201
rigid atoms, others: [34, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 811
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: REAL300025497238 none CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 28, 107, 107, 107, 107, 107, 1, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 1, 12, 12, 107, 1, 1] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 20, 36, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 32, 33, 34])
total number of confs: 243
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497238 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497238
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497238/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497238
Building REAL300025497239
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497239'
/scratch/stefan/7787277/working/building/REAL300025497239 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497239

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497239/0 /scratch/stefan/7787277/working/building/REAL300025497239 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 92)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/92
`/scratch/stefan/7787277/working/3D/92' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497239.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497239.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497239/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497239 none COCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
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, 114, 114, 114, 78, 78, 78, 78, 78, 62, 29, 62, 13, 1, 1, 1, 1, 1, 1, 1, 78, 201, 201, 201, 201, 201, 198, 198, 114, 78, 78, 78, 78, 78, 29, 29, 1, 78, 78] 201
rigid atoms, others: [38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 779
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: REAL300025497239 none COCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 18, 78, 78, 78, 78, 78, 1, 29, 29, 29, 23, 23, 20, 20, 5, 1, 1, 1, 1, 1, 9, 9, 78, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 210
number of broken/clashed sets: 84
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497239 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497239
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497239/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497239
Building REAL300025497240
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497240'
/scratch/stefan/7787277/working/building/REAL300025497240 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497240

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497240/0 /scratch/stefan/7787277/working/building/REAL300025497240 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 93)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/93
`/scratch/stefan/7787277/working/3D/93' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC2)C1)

`REAL300025497240.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497240.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497240/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497240 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 21, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 1, 4, 4, 4, 18, 18, 1, 13, 13, 83, 1, 1, 1, 1, 1, 4, 18, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [1, 36, 37, 10, 11, 12, 13, 14, 15, 21, 25, 26, 27, 28, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 22, 23, 24, 30, 31, 32, 33, 34, 35])
total number of confs: 178
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497240 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 17, 38, 72, 102, 201, 201, 201, 201, 201, 17, 17, 17, 17, 11, 11, 1, 11, 1, 1, 1, 17, 72, 72, 201, 17, 17, 17, 17, 17, 11, 1, 1, 1, 1, 1, 17, 17] 201
rigid atoms, others: [32, 33, 34, 35, 16, 18, 19, 20, 31] 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, 36, 37])
total number of confs: 486
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497240 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 37, 13, 1, 1, 1, 1, 1, 1, 1, 62, 83, 83, 83, 83, 83, 116, 116, 116, 201, 201, 83, 37, 37, 1, 83, 83, 83, 83, 83, 116, 201, 201, 201, 201, 201, 83, 83] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 24] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 693
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497240 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497240
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497240/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497240
Building REAL300025497241
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497241'
/scratch/stefan/7787277/working/building/REAL300025497241 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497241

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497241/0 /scratch/stefan/7787277/working/building/REAL300025497241 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 94)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/94
`/scratch/stefan/7787277/working/3D/94' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC2)C1)

`REAL300025497241.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497241.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497241/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497241 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 20, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 1, 13, 13, 71, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [1, 39, 40, 10, 11, 12, 13, 14, 15, 22, 26, 27, 28, 29, 30] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 167
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497241 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 19, 43, 80, 108, 201, 201, 201, 201, 201, 19, 19, 19, 19, 9, 9, 1, 9, 1, 1, 1, 1, 19, 80, 80, 201, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 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, 39, 40])
total number of confs: 504
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497241 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 39, 13, 1, 1, 1, 1, 1, 1, 1, 55, 71, 71, 71, 71, 71, 96, 96, 96, 201, 201, 201, 71, 39, 39, 1, 71, 71, 71, 71, 71, 96, 201, 201, 201, 201, 201, 201, 201, 71, 71] 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: 643
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497241 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497241
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497241/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497241
Building REAL300025497242
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497242'
/scratch/stefan/7787277/working/building/REAL300025497242 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497242

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497242/0 /scratch/stefan/7787277/working/building/REAL300025497242 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 95)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/95
`/scratch/stefan/7787277/working/3D/95' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC2)C1)

`REAL300025497242.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497242.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497242/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497242 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 20, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 19, 1, 13, 13, 73, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [1, 43, 10, 11, 12, 13, 14, 15, 42, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 175
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497242 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [44, 19, 44, 81, 110, 201, 201, 201, 201, 201, 19, 19, 19, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 19, 81, 81, 201, 19, 19, 19, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [33, 34, 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, 42, 43])
total number of confs: 516
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497242 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 35, 13, 1, 1, 1, 1, 1, 1, 1, 52, 73, 73, 73, 73, 73, 103, 103, 103, 201, 201, 201, 201, 73, 35, 35, 1, 73, 73, 73, 73, 73, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 73, 73] 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: 619
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497242 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497242
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497242/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497242
Building REAL300025497243
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497243'
/scratch/stefan/7787277/working/building/REAL300025497243 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497243

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497243/0 /scratch/stefan/7787277/working/building/REAL300025497243 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 96)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/96
`/scratch/stefan/7787277/working/3D/96' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCOCC2)C1)

`REAL300025497243.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497243.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497243/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497243 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCOCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 13, 21, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 1, 13, 13, 67, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 43, 44, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 168
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497243 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCOCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 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, 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: [40, 18, 40, 75, 102, 201, 201, 201, 201, 201, 18, 18, 18, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 75, 75, 201, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [34, 35, 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, 43, 44])
total number of confs: 497
number of broken/clashed sets: 24
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497243 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCOCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 33, 13, 1, 1, 1, 1, 1, 1, 1, 48, 67, 67, 67, 67, 67, 96, 96, 96, 201, 201, 201, 201, 201, 67, 33, 33, 1, 67, 67, 67, 67, 67, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201, 67, 67] 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: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497243 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497243
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497243/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497243
Building REAL300025497244
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497244'
/scratch/stefan/7787277/working/building/REAL300025497244 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497244

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497244/0 /scratch/stefan/7787277/working/building/REAL300025497244 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 97)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/97
`/scratch/stefan/7787277/working/3D/97' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497244.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497244.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497244/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497244 none O=C(CC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
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: [5, 5, 5, 26, 39, 39, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 8, 20, 20, 20, 20, 20, 1, 26, 26, 39, 39, 39, 39, 39, 5, 1, 1, 1, 1, 1, 7, 7, 20, 1, 1] 60
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 178
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497244 none O=C(CC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
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: [32, 32, 32, 50, 60, 60, 20, 20, 20, 20, 20, 20, 20, 20, 12, 1, 1, 1, 1, 1, 1, 1, 20, 50, 50, 60, 60, 60, 60, 60, 32, 20, 20, 20, 20, 20, 20, 20, 1, 20, 20] 60
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])
total number of confs: 235
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497244 none O=C(CC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [19, 3, 1, 1, 1, 1, 19, 19, 39, 39, 39, 39, 39, 55, 55, 55, 55, 60, 60, 60, 60, 60, 39, 3, 3, 1, 1, 1, 1, 1, 19, 39, 39, 39, 39, 39, 55, 55, 60, 39, 39] 60
rigid atoms, others: [2, 3, 4, 5, 25, 26, 27, 28, 29] set([0, 1, 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])
total number of confs: 172
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497244 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497244
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497244/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497244
Building REAL300025497245
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497245'
/scratch/stefan/7787277/working/building/REAL300025497245 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497245

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497245/0 /scratch/stefan/7787277/working/building/REAL300025497245 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 98)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/98
`/scratch/stefan/7787277/working/3D/98' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497245.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497245.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497245/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497245 none CC(C)(F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 197, 201, 201, 197, 197, 138, 138, 138, 138, 138, 111, 45, 111, 13, 1, 1, 1, 1, 1, 1, 1, 138, 201, 201, 201, 201, 201, 201, 197, 138, 138, 138, 138, 138, 45, 45, 1, 138, 138] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 633
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: REAL300025497245 none CC(C)(F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [16, 5, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 35, 138, 138, 138, 138, 138, 1, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 14, 14, 138, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 6, 7, 8, 9, 10, 11, 12, 22, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 268
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497245 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497245
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497245/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497245
Building REAL300025497246
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497246'
/scratch/stefan/7787277/working/building/REAL300025497246 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497246

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497246/0 /scratch/stefan/7787277/working/building/REAL300025497246 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 99)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/99
`/scratch/stefan/7787277/working/3D/99' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(F)(F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497246.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497246.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497246/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497246 none CC(F)(F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 15, 15, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 148, 201, 201, 148, 148, 112, 112, 112, 112, 112, 91, 50, 91, 13, 1, 1, 1, 1, 1, 1, 1, 112, 201, 201, 201, 148, 112, 112, 112, 112, 112, 50, 50, 1, 112, 112] 201
rigid atoms, others: [34, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 784
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: REAL300025497246 none CC(F)(F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 15, 15, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 18, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 26, 112, 112, 112, 112, 112, 1, 18, 18, 18, 5, 1, 1, 1, 1, 1, 11, 11, 112, 1, 1] 201
rigid atoms, others: [35, 36, 6, 7, 8, 9, 10, 11, 12, 22, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 32, 33, 34])
total number of confs: 230
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497246 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497246
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497246/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497246
Building REAL300025497247
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497247'
/scratch/stefan/7787277/working/building/REAL300025497247 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497247

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497247/0 /scratch/stefan/7787277/working/building/REAL300025497247 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 100)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/100
`/scratch/stefan/7787277/working/3D/100' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497247.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497247.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497247/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497247 none COCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
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, 91, 91, 91, 91, 91, 80, 54, 80, 13, 1, 1, 1, 1, 1, 1, 1, 91, 201, 201, 201, 201, 201, 133, 91, 91, 91, 91, 91, 54, 54, 1, 91, 91] 201
rigid atoms, others: [35, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 839
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: REAL300025497247 none COCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 17, 91, 91, 91, 91, 91, 1, 30, 30, 30, 23, 23, 5, 1, 1, 1, 1, 1, 10, 10, 91, 1, 1] 201
rigid atoms, others: [32, 36, 5, 6, 7, 8, 9, 10, 11, 37, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 33, 34, 35])
total number of confs: 223
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497247 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497247
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497247/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497247
Building REAL300025497248
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497248'
/scratch/stefan/7787277/working/building/REAL300025497248 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497248

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497248/0 /scratch/stefan/7787277/working/building/REAL300025497248 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 101)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/101
`/scratch/stefan/7787277/working/3D/101' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC=N2)C1)

`REAL300025497248.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497248.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497248/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497248 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 22, 46, 132, 132, 132, 132, 132, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 22, 22, 132, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 38, 39, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37])
total number of confs: 250
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497248 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 25, 59, 98, 201, 201, 201, 201, 201, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 59, 59, 201, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 8, 8] 201
rigid atoms, others: [34, 35, 36, 37, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 445
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497248 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [98, 40, 13, 1, 1, 1, 1, 1, 1, 1, 98, 132, 132, 132, 132, 132, 201, 201, 201, 201, 201, 201, 201, 201, 132, 40, 40, 1, 132, 132, 132, 132, 132, 201, 201, 201, 201, 201, 132, 132] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 626
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497248 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497248
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497248/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497248
Building REAL300025497249
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497249'
/scratch/stefan/7787277/working/building/REAL300025497249 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497249

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497249/0 /scratch/stefan/7787277/working/building/REAL300025497249 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 102)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/102
`/scratch/stefan/7787277/working/3D/102' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NC=C2)C1)

`REAL300025497249.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497249.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497249/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497249 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 18, 41, 138, 138, 138, 138, 138, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 18, 18, 138, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 38, 39, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37])
total number of confs: 244
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497249 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 8, 30, 71, 124, 201, 201, 201, 201, 201, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 71, 71, 201, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 8, 8] 201
rigid atoms, others: [34, 35, 36, 37, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 488
number of broken/clashed sets: 29
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497249 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [99, 51, 13, 1, 1, 1, 1, 1, 1, 1, 99, 138, 138, 138, 138, 138, 201, 201, 201, 201, 201, 201, 201, 201, 138, 51, 51, 1, 138, 138, 138, 138, 138, 201, 201, 201, 201, 201, 138, 138] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 619
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497249 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497249
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497249/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497249
Building REAL300025497250
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497250'
/scratch/stefan/7787277/working/building/REAL300025497250 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497250

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497250/0 /scratch/stefan/7787277/working/building/REAL300025497250 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 103)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/103
`/scratch/stefan/7787277/working/3D/103' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)C=C2)C1)

`REAL300025497250.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497250.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497250/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497250 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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, 18, 41, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 5, 8, 8, 8, 1, 18, 18, 135, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 33, 40, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38])
total number of confs: 257
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497250 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [32, 8, 32, 73, 127, 201, 201, 201, 201, 201, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 8, 73, 73, 201, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 8, 8] 201
rigid atoms, others: [35, 36, 37, 38, 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, 39, 40])
total number of confs: 493
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497250 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [97, 51, 13, 1, 1, 1, 1, 1, 1, 1, 97, 135, 135, 135, 135, 135, 201, 201, 201, 201, 201, 201, 201, 201, 201, 135, 51, 51, 1, 135, 135, 135, 135, 135, 201, 201, 201, 201, 201, 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])
total number of confs: 619
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497250 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497250
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497250/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497250
Building REAL300025497251
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497251'
/scratch/stefan/7787277/working/building/REAL300025497251 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497251

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497251/0 /scratch/stefan/7787277/working/building/REAL300025497251 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 104)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/104
`/scratch/stefan/7787277/working/3D/104' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497251.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497251.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497251/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497251 none CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need 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, 107, 107, 107, 72, 72, 72, 72, 72, 56, 43, 56, 13, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 201, 195, 195, 107, 72, 72, 72, 72, 72, 43, 43, 1, 72, 72] 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])
total number of confs: 854
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: REAL300025497251 none CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 20, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 72, 72, 72, 72, 72, 1, 31, 31, 31, 31, 31, 20, 20, 4, 1, 1, 1, 1, 1, 9, 9, 72, 1, 1] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 21, 39, 38, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 266
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497251 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497251
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497251/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497251
Building REAL300025497252
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497252'
/scratch/stefan/7787277/working/building/REAL300025497252 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497252

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497252/0 /scratch/stefan/7787277/working/building/REAL300025497252 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 105)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/105
`/scratch/stefan/7787277/working/3D/105' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN=C2)C1)

`REAL300025497252.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497252.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497252/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497252 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [5, 1, 5, 14, 30, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 1, 14, 14, 102, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 1, 1] 201
rigid atoms, others: [32, 1, 38, 39, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37])
total number of confs: 199
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497252 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [41, 14, 41, 82, 126, 201, 201, 201, 201, 201, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 82, 82, 201, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 14, 14] 201
rigid atoms, others: [34, 35, 36, 37, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39])
total number of confs: 529
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497252 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [71, 43, 13, 1, 1, 1, 1, 1, 1, 1, 71, 102, 102, 102, 102, 102, 144, 144, 144, 201, 201, 201, 201, 201, 102, 43, 43, 1, 102, 102, 102, 102, 102, 144, 201, 201, 201, 201, 102, 102] 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: 561
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497252 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497252
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497252/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497252
Building REAL300025497253
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497253'
/scratch/stefan/7787277/working/building/REAL300025497253 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497253

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497253/0 /scratch/stefan/7787277/working/building/REAL300025497253 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 106)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/106
`/scratch/stefan/7787277/working/3D/106' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CC=CS1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497253.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497253.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497253/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497253 none O=C(CC1=CC=CS1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 14, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 23, 86, 86, 86, 86, 86, 1, 21, 21, 29, 29, 29, 4, 1, 1, 1, 1, 1, 13, 13, 86, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 227
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497253 none O=C(CC1=CC=CS1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 14, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 186, 201, 201, 201, 201, 86, 86, 86, 86, 86, 53, 30, 53, 13, 1, 1, 1, 1, 1, 1, 1, 86, 186, 186, 201, 201, 201, 109, 86, 86, 86, 86, 86, 30, 30, 1, 86, 86] 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])
total number of confs: 737
number of broken/clashed sets: 36
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497253 none O=C(CC1=CC=CS1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 14, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 18, 18, 29, 29, 29, 29, 29, 49, 49, 87, 124, 201, 201, 201, 201, 201, 29, 3, 3, 1, 1, 1, 18, 29, 29, 29, 29, 29, 87, 87, 201, 29, 29] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 539
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497253 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497253
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497253/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497253
Building REAL300025497254
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497254'
/scratch/stefan/7787277/working/building/REAL300025497254 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497254

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497254/0 /scratch/stefan/7787277/working/building/REAL300025497254 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 107)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/107
`/scratch/stefan/7787277/working/3D/107' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CO2)C1)

`REAL300025497254.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497254.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497254/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497254 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 22, 48, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 1, 22, 22, 135, 1, 1, 1, 1, 1, 6, 10, 10, 10, 1, 1] 201
rigid atoms, others: [1, 36, 37, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34, 35])
total number of confs: 257
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497254 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 10, 27, 63, 103, 201, 201, 201, 201, 201, 10, 10, 10, 10, 5, 5, 1, 5, 1, 1, 1, 1, 1, 10, 63, 63, 201, 10, 10, 10, 10, 10, 5, 1, 1, 1, 10, 10] 201
rigid atoms, others: [33, 34, 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, 36, 37])
total number of confs: 451
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497254 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [104, 43, 13, 1, 1, 1, 1, 1, 1, 1, 104, 135, 135, 135, 135, 135, 197, 197, 197, 201, 201, 201, 201, 135, 43, 43, 1, 135, 135, 135, 135, 135, 197, 201, 201, 201, 135, 135] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 625
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497254 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497254
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497254/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497254
Building REAL300025497255
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497255'
/scratch/stefan/7787277/working/building/REAL300025497255 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497255

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497255/0 /scratch/stefan/7787277/working/building/REAL300025497255 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 108)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/108
`/scratch/stefan/7787277/working/3D/108' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497255.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497255.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497255/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497255 none CC(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  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, 102, 102, 102, 79, 79, 79, 79, 79, 53, 29, 53, 13, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 199, 199, 102, 79, 79, 79, 79, 79, 29, 29, 1, 79, 79] 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])
total number of confs: 757
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497255 none CC(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 27, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 20, 79, 79, 79, 79, 79, 1, 40, 40, 40, 40, 27, 27, 4, 1, 1, 1, 1, 1, 10, 10, 79, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 40, 23, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 254
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497255 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497255
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497255/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497255
Building REAL300025497256
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497256'
/scratch/stefan/7787277/working/building/REAL300025497256 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497256

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497256/0 /scratch/stefan/7787277/working/building/REAL300025497256 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 109)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/109
`/scratch/stefan/7787277/working/3D/109' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=C1)

`REAL300025497256.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497256.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497256/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497256 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 1, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 30, 101, 101, 101, 101, 101, 1, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 13, 13, 101, 1, 1, 16, 16] 201
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 37, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40])
total number of confs: 195
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497256 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 1, 7, 7, 7, 6, 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]
0  hydrogens need rotated
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, 101, 101, 101, 101, 101, 85, 41, 85, 13, 1, 1, 1, 1, 1, 1, 1, 101, 201, 201, 201, 201, 201, 201, 133, 101, 101, 101, 101, 101, 41, 41, 1, 101, 101, 201, 201] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 543
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497256 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 1, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 16, 16, 16, 16, 16, 32, 32, 66, 111, 201, 201, 201, 201, 201, 16, 1, 1, 1, 2, 2, 2, 7, 16, 16, 16, 16, 16, 66, 66, 201, 16, 16, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 39, 40, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 499
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497256 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497256
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497256/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497256
Building REAL300025497257
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497257'
/scratch/stefan/7787277/working/building/REAL300025497257 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497257

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497257/0 /scratch/stefan/7787277/working/building/REAL300025497257 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 110)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/110
`/scratch/stefan/7787277/working/3D/110' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1)

`REAL300025497257.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497257.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497257/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497257 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 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: [14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 55, 148, 148, 148, 148, 148, 1, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 32, 32, 148, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 40, 23, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 309
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497257 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 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, 191, 191, 191, 148, 148, 148, 148, 148, 109, 43, 109, 13, 1, 1, 1, 1, 1, 1, 1, 148, 201, 201, 201, 201, 201, 201, 191, 148, 148, 148, 148, 148, 43, 43, 1, 148, 148] 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])
total number of confs: 595
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497257 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 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, 5, 5, 5, 14, 14, 14, 14, 14, 40, 40, 96, 128, 201, 201, 201, 201, 201, 14, 1, 2, 2, 2, 1, 1, 5, 14, 14, 14, 14, 14, 96, 96, 201, 14, 14] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 550
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497257 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497257
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497257/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497257
Building REAL300025497258
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497258'
/scratch/stefan/7787277/working/building/REAL300025497258 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497258

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497258/0 /scratch/stefan/7787277/working/building/REAL300025497258 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 111)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/111
`/scratch/stefan/7787277/working/3D/111' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=CC1=CC=CO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497258.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497258.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497258/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497258 none O=C(C=CC1=CC=CO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 12, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 19, 19, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 49, 138, 138, 138, 138, 138, 1, 19, 19, 24, 24, 24, 5, 1, 1, 1, 1, 1, 23, 23, 138, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 300
number of broken/clashed sets: 58
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497258 none O=C(C=CC1=CC=CO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 12, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 174, 174, 201, 201, 201, 201, 201, 201, 138, 138, 138, 138, 138, 89, 32, 89, 13, 1, 1, 1, 1, 1, 1, 1, 138, 201, 201, 201, 201, 201, 174, 138, 138, 138, 138, 138, 32, 32, 1, 138, 138] 201
rigid atoms, others: [39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41])
total number of confs: 582
number of broken/clashed sets: 58
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497258 none O=C(C=CC1=CC=CO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 1, 1, 1, 1, 1, 1, 12, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 13, 13, 24, 24, 24, 24, 24, 37, 37, 81, 123, 201, 201, 201, 201, 201, 24, 4, 4, 1, 1, 1, 13, 24, 24, 24, 24, 24, 81, 81, 201, 24, 24] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 28, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 503
number of broken/clashed sets: 58
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497258 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497258
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497258/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497258
Building REAL300025497259
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497259'
/scratch/stefan/7787277/working/building/REAL300025497259 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497259

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497259/0 /scratch/stefan/7787277/working/building/REAL300025497259 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 112)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/112
`/scratch/stefan/7787277/working/3D/112' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC=C2F)C1)

`REAL300025497259.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497259.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497259/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497259 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC=C2F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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, 19, 40, 134, 134, 134, 134, 134, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 7, 16, 16, 16, 1, 19, 19, 134, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 1, 1] 201
rigid atoms, others: [32, 1, 33, 40, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38])
total number of confs: 285
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497259 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC=C2F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [38, 16, 38, 74, 110, 201, 201, 201, 201, 201, 16, 16, 16, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 16, 74, 74, 201, 16, 16, 16, 16, 16, 8, 1, 1, 1, 1, 16, 16] 201
rigid atoms, others: [35, 36, 37, 38, 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, 39, 40])
total number of confs: 476
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497259 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC=C2F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 15, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [93, 40, 13, 1, 1, 1, 1, 1, 1, 1, 93, 134, 134, 134, 134, 134, 191, 191, 191, 201, 201, 201, 201, 201, 201, 134, 40, 40, 1, 134, 134, 134, 134, 134, 191, 201, 201, 201, 201, 134, 134] 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: 588
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497259 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497259
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497259/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497259
Building REAL300025497260
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497260'
/scratch/stefan/7787277/working/building/REAL300025497260 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497260

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497260/0 /scratch/stefan/7787277/working/building/REAL300025497260 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 113)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/113
`/scratch/stefan/7787277/working/3D/113' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC=C2)C1)

`REAL300025497260.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497260.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497260/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497260 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 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]
0  hydrogens 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, 39, 136, 136, 136, 136, 136, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 5, 8, 8, 1, 17, 17, 136, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 39, 40, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38])
total number of confs: 256
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497260 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 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]
0  hydrogens 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, 28, 69, 125, 201, 201, 201, 201, 201, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 69, 69, 201, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 8, 8] 201
rigid atoms, others: [34, 35, 36, 37, 38, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40])
total number of confs: 487
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497260 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 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]
0  hydrogens 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, 50, 13, 1, 1, 1, 1, 1, 1, 1, 99, 136, 136, 136, 136, 136, 201, 201, 201, 201, 201, 201, 201, 201, 136, 50, 50, 1, 136, 136, 136, 136, 136, 201, 201, 201, 201, 201, 201, 136, 136] 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: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497260 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497260
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497260/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497260
Building REAL300025497261
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497261'
/scratch/stefan/7787277/working/building/REAL300025497261 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497261

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497261/0 /scratch/stefan/7787277/working/building/REAL300025497261 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 114)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/114
`/scratch/stefan/7787277/working/3D/114' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497261.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497261.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497261/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497261 none CC(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 117, 117, 117, 78, 78, 78, 78, 78, 61, 40, 61, 13, 1, 1, 1, 1, 1, 1, 1, 78, 201, 201, 201, 201, 201, 201, 201, 201, 201, 117, 78, 78, 78, 78, 78, 40, 40, 1, 78, 78] 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])
total number of confs: 823
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: REAL300025497261 none CC(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [19, 17, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 24, 78, 78, 78, 78, 78, 1, 21, 21, 21, 21, 21, 21, 21, 17, 17, 5, 1, 1, 1, 1, 1, 11, 11, 78, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 229
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497261 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497261
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497261/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497261
Building REAL300025497262
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497262'
/scratch/stefan/7787277/working/building/REAL300025497262 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497262

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497262/0 /scratch/stefan/7787277/working/building/REAL300025497262 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 115)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/115
`/scratch/stefan/7787277/working/3D/115' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCCC2)C1)

`REAL300025497262.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497262.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497262/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497262 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 18, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 1, 12, 12, 60, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 45, 10, 11, 12, 13, 14, 15, 46, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 154
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497262 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 18, 47, 83, 113, 201, 201, 201, 201, 201, 18, 18, 18, 18, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 18, 83, 83, 201, 18, 18, 18, 18, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [34, 35, 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, 45, 46])
total number of confs: 518
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497262 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 31, 13, 1, 1, 1, 1, 1, 1, 1, 43, 60, 60, 60, 60, 60, 90, 90, 90, 201, 201, 201, 201, 201, 60, 31, 31, 1, 60, 60, 60, 60, 60, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 60, 60] 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: 622
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497262 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497262
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497262/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497262
Building REAL300025497263
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497263'
/scratch/stefan/7787277/working/building/REAL300025497263 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497263

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497263/0 /scratch/stefan/7787277/working/building/REAL300025497263 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 116)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/116
`/scratch/stefan/7787277/working/3D/116' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CC=N2)C1)

`REAL300025497263.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497263.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497263/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497263 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 5, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 22, 47, 132, 132, 132, 132, 132, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 22, 22, 132, 1, 1, 1, 1, 1, 5, 8, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 37, 38, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36])
total number of confs: 247
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497263 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 5, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 8, 25, 58, 99, 201, 201, 201, 201, 201, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 58, 58, 201, 8, 8, 8, 8, 8, 3, 1, 1, 1, 8, 8] 201
rigid atoms, others: [34, 35, 36, 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, 37, 38])
total number of confs: 444
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497263 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 5, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [99, 41, 13, 1, 1, 1, 1, 1, 1, 1, 99, 132, 132, 132, 132, 132, 201, 201, 201, 201, 201, 201, 201, 201, 132, 41, 41, 1, 132, 132, 132, 132, 132, 201, 201, 201, 201, 132, 132] 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: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497263 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497263
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497263/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497263
Building REAL300025497264
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497264'
/scratch/stefan/7787277/working/building/REAL300025497264 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497264

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497264/0 /scratch/stefan/7787277/working/building/REAL300025497264 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 117)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/117
`/scratch/stefan/7787277/working/3D/117' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497264.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497264.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497264/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497264 none CC1=CC=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 10, 22, 22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 30, 72, 72, 72, 72, 72, 1, 22, 22, 22, 22, 21, 22, 22, 5, 1, 1, 1, 1, 1, 18, 18, 72, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 225
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497264 none CC1=CC=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 91, 91, 91, 72, 72, 72, 72, 72, 58, 34, 58, 13, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 201, 201, 201, 91, 72, 72, 72, 72, 72, 34, 34, 1, 72, 72] 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])
total number of confs: 472
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497264 none CC1=CC=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 22, 22, 22, 22, 22, 53, 53, 91, 135, 201, 201, 201, 201, 201, 22, 2, 2, 2, 1, 1, 1, 1, 9, 22, 22, 22, 22, 22, 91, 91, 201, 22, 22] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 549
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497264 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497264
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497264/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497264
Building REAL300025497265
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497265'
/scratch/stefan/7787277/working/building/REAL300025497265 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497265

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497265/0 /scratch/stefan/7787277/working/building/REAL300025497265 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 118)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/118
`/scratch/stefan/7787277/working/3D/118' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497265.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497265.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497265/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497265 none O=C(CC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 54, 54, 54, 54, 54, 1, 27, 27, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 1, 1, 1, 1, 1, 6, 6, 54, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 233
number of broken/clashed sets: 56
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497265 none O=C(CC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 196, 201, 201, 201, 201, 54, 54, 54, 54, 54, 49, 31, 49, 13, 1, 1, 1, 1, 1, 1, 1, 54, 196, 196, 201, 201, 201, 201, 201, 201, 201, 201, 201, 91, 54, 54, 54, 54, 54, 31, 31, 1, 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])
total number of confs: 797
number of broken/clashed sets: 56
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497265 none O=C(CC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 5, 1, 1, 1, 1, 1, 1, 22, 22, 45, 45, 45, 45, 45, 53, 53, 104, 145, 201, 201, 201, 201, 201, 45, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 45, 45, 45, 45, 45, 104, 104, 201, 45, 45] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 34, 35, 27, 28, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 589
number of broken/clashed sets: 56
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497265 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497265
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497265/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497265
Building REAL300025497266
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497266'
/scratch/stefan/7787277/working/building/REAL300025497266 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497266

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497266/0 /scratch/stefan/7787277/working/building/REAL300025497266 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 119)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/119
`/scratch/stefan/7787277/working/3D/119' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497266.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497266.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497266/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497266 none O=C(CCC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 16, 19, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 44, 44, 44, 44, 44, 1, 16, 16, 21, 21, 39, 39, 39, 39, 39, 39, 39, 39, 39, 3, 1, 1, 1, 1, 1, 5, 5, 44, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 217
number of broken/clashed sets: 69
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497266 none O=C(CCC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 159, 140, 201, 201, 201, 201, 44, 44, 44, 44, 44, 38, 29, 38, 13, 1, 1, 1, 1, 1, 1, 1, 44, 159, 159, 163, 163, 201, 201, 201, 201, 201, 201, 201, 201, 201, 46, 44, 44, 44, 44, 44, 29, 29, 1, 44, 44] 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: 881
number of broken/clashed sets: 69
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497266 none O=C(CCC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 7, 4, 1, 1, 1, 1, 1, 1, 28, 28, 39, 39, 39, 39, 39, 43, 43, 88, 132, 201, 201, 201, 201, 201, 39, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 39, 39, 39, 39, 39, 88, 88, 201, 39, 39] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 35, 36, 38, 37, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 556
number of broken/clashed sets: 69
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497266 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497266
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497266/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497266
Building REAL300025497267
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497267'
/scratch/stefan/7787277/working/building/REAL300025497267 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497267

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497267/0 /scratch/stefan/7787277/working/building/REAL300025497267 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 120)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/120
`/scratch/stefan/7787277/working/3D/120' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC(F)=C2)C1)

`REAL300025497267.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497267.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497267/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497267 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC(F)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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, 13, 21, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 14, 1, 13, 13, 58, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 1, 1] 201
rigid atoms, others: [32, 1, 33, 40, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38])
total number of confs: 138
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497267 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC(F)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [36, 14, 36, 76, 111, 201, 201, 201, 201, 201, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 76, 76, 201, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 14, 14] 201
rigid atoms, others: [35, 36, 37, 38, 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, 39, 40])
total number of confs: 503
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497267 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC(F)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 15, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [45, 34, 12, 1, 1, 1, 1, 1, 1, 1, 45, 58, 58, 58, 58, 58, 79, 79, 79, 201, 201, 201, 201, 201, 201, 58, 34, 34, 1, 58, 58, 58, 58, 58, 79, 201, 201, 201, 201, 58, 58] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 437
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497267 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497267
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497267/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497267
Building REAL300025497268
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497268'
/scratch/stefan/7787277/working/building/REAL300025497268 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497268

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497268/0 /scratch/stefan/7787277/working/building/REAL300025497268 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 121)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/121
`/scratch/stefan/7787277/working/3D/121' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CS2)C1)

`REAL300025497268.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497268.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497268/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497268 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 14, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 129, 129, 129, 129, 129, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 1, 19, 19, 129, 1, 1, 1, 1, 1, 5, 12, 12, 12, 1, 1] 201
rigid atoms, others: [1, 36, 37, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34, 35])
total number of confs: 243
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497268 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 14, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 12, 28, 61, 99, 201, 201, 201, 201, 201, 12, 12, 12, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 12, 61, 61, 201, 12, 12, 12, 12, 12, 5, 1, 1, 1, 12, 12] 201
rigid atoms, others: [33, 34, 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, 36, 37])
total number of confs: 454
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497268 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 14, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 43, 13, 1, 1, 1, 1, 1, 1, 1, 96, 129, 129, 129, 129, 129, 181, 181, 181, 201, 201, 201, 201, 129, 43, 43, 1, 129, 129, 129, 129, 129, 181, 201, 201, 201, 129, 129] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 611
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497268 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497268
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497268/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497268
Building REAL300025497269
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497269'
/scratch/stefan/7787277/working/building/REAL300025497269 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497269

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497269/0 /scratch/stefan/7787277/working/building/REAL300025497269 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 122)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/122
`/scratch/stefan/7787277/working/3D/122' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1)

`REAL300025497269.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497269.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497269/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497269 none CC1=CN=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 55, 150, 150, 150, 150, 150, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 32, 32, 150, 1, 1, 11] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 40, 23, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41])
total number of confs: 309
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497269 none CC1=CN=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 150, 150, 150, 150, 150, 112, 47, 112, 13, 1, 1, 1, 1, 1, 1, 1, 150, 201, 201, 201, 201, 201, 201, 201, 150, 150, 150, 150, 150, 47, 47, 1, 150, 150, 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])
total number of confs: 613
number of broken/clashed sets: 32
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497269 none CC1=CN=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 31, 31, 89, 123, 201, 201, 201, 201, 201, 11, 1, 1, 2, 2, 2, 1, 4, 11, 11, 11, 11, 11, 89, 89, 201, 11, 11, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 24, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 533
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497269 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497269
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497269/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497269
Building REAL300025497270
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497270'
/scratch/stefan/7787277/working/building/REAL300025497270 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497270

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497270/0 /scratch/stefan/7787277/working/building/REAL300025497270 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 123)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/123
`/scratch/stefan/7787277/working/3D/123' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CSC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497270.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497270.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497270/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497270 none O=C(CC1=CSC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 15, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 19, 47, 47, 47, 47, 47, 1, 15, 15, 28, 28, 28, 5, 1, 1, 1, 1, 1, 14, 14, 47, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 176
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497270 none O=C(CC1=CSC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 111, 201, 201, 201, 201, 47, 47, 47, 47, 47, 46, 32, 46, 13, 1, 1, 1, 1, 1, 1, 1, 47, 111, 111, 201, 201, 201, 57, 47, 47, 47, 47, 47, 32, 32, 1, 47, 47] 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])
total number of confs: 636
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497270 none O=C(CC1=CSC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 28, 28, 28, 28, 28, 56, 56, 98, 131, 201, 201, 201, 201, 201, 28, 2, 2, 1, 1, 1, 9, 28, 28, 28, 28, 28, 98, 98, 201, 28, 28] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 556
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497270 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497270
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497270/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497270
Building REAL300025497271
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497271'
/scratch/stefan/7787277/working/building/REAL300025497271 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497271

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497271/0 /scratch/stefan/7787277/working/building/REAL300025497271 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 124)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/124
`/scratch/stefan/7787277/working/3D/124' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497271.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497271.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497271/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497271 none CC1CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 29, 104, 104, 104, 104, 104, 1, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 15, 15, 104, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 213
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497271 none CC1CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 143, 143, 143, 104, 104, 104, 104, 104, 85, 43, 85, 13, 1, 1, 1, 1, 1, 1, 1, 104, 201, 201, 201, 201, 201, 201, 201, 143, 104, 104, 104, 104, 104, 43, 43, 1, 104, 104] 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])
total number of confs: 673
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497271 none CC1CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 15, 15, 15, 15, 15, 42, 42, 77, 121, 201, 201, 201, 201, 201, 15, 2, 2, 2, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 77, 77, 201, 15, 15] 201
rigid atoms, others: [0, 1, 2, 3, 4, 26, 27, 28, 29] set([5, 6, 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])
total number of confs: 507
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497271 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497271
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497271/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497271
Building REAL300025497272
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497272'
/scratch/stefan/7787277/working/building/REAL300025497272 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497272

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497272/0 /scratch/stefan/7787277/working/building/REAL300025497272 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 125)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/125
`/scratch/stefan/7787277/working/3D/125' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497272.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497272.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497272/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497272 none CC1=CC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 24, 65, 65, 65, 65, 65, 1, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 14, 14, 65, 1, 1, 15] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 153
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497272 none CC1=CC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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, 77, 77, 77, 65, 65, 65, 65, 65, 50, 35, 50, 10, 1, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 201, 201, 77, 65, 65, 65, 65, 65, 35, 35, 1, 65, 65, 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])
total number of confs: 434
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497272 none CC1=CC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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, 15, 15, 15, 15, 15, 37, 37, 74, 115, 201, 201, 201, 201, 201, 15, 1, 2, 2, 2, 1, 1, 1, 5, 15, 15, 15, 15, 15, 74, 74, 201, 15, 15, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 43, 25, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 516
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497272 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497272
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497272/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497272
Building REAL300025497273
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497273'
/scratch/stefan/7787277/working/building/REAL300025497273 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497273

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497273/0 /scratch/stefan/7787277/working/building/REAL300025497273 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 126)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/126
`/scratch/stefan/7787277/working/3D/126' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497273.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497273.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497273/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497273 none CCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 105, 105, 105, 71, 71, 71, 71, 71, 55, 28, 55, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 201, 201, 105, 71, 71, 71, 71, 71, 28, 28, 1, 71, 71] 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])
total number of confs: 780
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497273 none CCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 20, 71, 71, 71, 71, 71, 1, 35, 35, 35, 35, 35, 21, 21, 5, 1, 1, 1, 1, 1, 9, 9, 71, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 206
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497273 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497273
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497273/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497273
Building REAL300025497274
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497274'
/scratch/stefan/7787277/working/building/REAL300025497274 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497274

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497274/0 /scratch/stefan/7787277/working/building/REAL300025497274 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 127)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/127
`/scratch/stefan/7787277/working/3D/127' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497274.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497274.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497274/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497274 none CC(C)=CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  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, 89, 89, 89, 89, 89, 75, 38, 75, 13, 1, 1, 1, 1, 1, 1, 1, 89, 201, 201, 201, 201, 201, 201, 201, 123, 89, 89, 89, 89, 89, 38, 38, 1, 89, 89] 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])
total number of confs: 693
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: REAL300025497274 none CC(C)=CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 5, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 25, 89, 89, 89, 89, 89, 1, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 13, 13, 89, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 188
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497274 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497274
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497274/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497274
Building REAL300025497275
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497275'
/scratch/stefan/7787277/working/building/REAL300025497275 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497275

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497275/0 /scratch/stefan/7787277/working/building/REAL300025497275 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 128)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/128
`/scratch/stefan/7787277/working/3D/128' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COCCO2)C1)

`REAL300025497275.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497275.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497275/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497275 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 7, 7, 6, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 21, 42, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 1, 21, 21, 130, 1, 1, 1, 1, 1, 5, 10, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [32, 1, 39, 40, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38])
total number of confs: 245
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497275 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 7, 7, 6, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 10, 26, 59, 93, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 59, 59, 201, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [34, 35, 36, 37, 38, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40])
total number of confs: 440
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497275 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 7, 7, 6, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [97, 40, 13, 1, 1, 1, 1, 1, 1, 1, 97, 130, 130, 130, 130, 130, 201, 201, 201, 201, 201, 201, 201, 201, 130, 40, 40, 1, 130, 130, 130, 130, 130, 201, 201, 201, 201, 201, 201, 130, 130] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 622
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497275 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497275
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497275/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497275
Building REAL300025497276
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497276'
/scratch/stefan/7787277/working/building/REAL300025497276 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497276

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497276/0 /scratch/stefan/7787277/working/building/REAL300025497276 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 129)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/129
`/scratch/stefan/7787277/working/3D/129' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=[N+]([O-])C=C2)C1)

`REAL300025497276.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497276.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497276/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497276 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=[N+]([O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 38, 133, 133, 133, 133, 133, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 5, 5, 8, 8, 1, 18, 18, 133, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 33, 40, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38])
total number of confs: 246
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497276 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=[N+]([O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 8, 32, 71, 121, 201, 201, 201, 201, 201, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 8, 71, 71, 201, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 8, 8] 201
rigid atoms, others: [35, 36, 37, 38, 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, 39, 40])
total number of confs: 487
number of broken/clashed sets: 33
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497276 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=[N+]([O-])C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 12, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [92, 50, 13, 1, 1, 1, 1, 1, 1, 1, 92, 133, 133, 133, 133, 133, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 50, 50, 1, 133, 133, 133, 133, 133, 201, 201, 201, 201, 201, 133, 133] 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: 622
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497276 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497276
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497276/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497276
Building REAL300025497277
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497277'
/scratch/stefan/7787277/working/building/REAL300025497277 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497277

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497277/0 /scratch/stefan/7787277/working/building/REAL300025497277 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 130)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/130
`/scratch/stefan/7787277/working/3D/130' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3C=CC2C3)C1)

`REAL300025497277.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497277.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497277/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497277 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3C=CC2C3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 33, 110, 110, 110, 110, 110, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 18, 1, 16, 16, 110, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 45, 33, 44, 10, 11, 12, 13, 14, 15, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 229
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497277 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3C=CC2C3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 18, 36, 71, 108, 201, 201, 201, 201, 201, 18, 18, 18, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 18, 71, 71, 201, 18, 18, 18, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [35, 36, 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, 44, 45])
total number of confs: 484
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497277 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3C=CC2C3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 45, 13, 1, 1, 1, 1, 1, 1, 1, 81, 110, 110, 110, 110, 110, 153, 153, 153, 201, 201, 201, 201, 201, 201, 110, 45, 45, 1, 110, 110, 110, 110, 110, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 110] 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: 670
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497277 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497277
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497277/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497277
Building REAL300025497278
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497278'
/scratch/stefan/7787277/working/building/REAL300025497278 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497278

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497278/0 /scratch/stefan/7787277/working/building/REAL300025497278 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 131)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/131
`/scratch/stefan/7787277/working/3D/131' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497278.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497278.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497278/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497278 none CC(=O)NC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 201, 144, 144, 94, 94, 94, 94, 94, 62, 26, 61, 13, 1, 1, 1, 1, 1, 1, 1, 94, 201, 201, 201, 201, 201, 201, 201, 201, 144, 94, 94, 94, 94, 94, 26, 26, 1, 94, 94] 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])
total number of confs: 719
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: REAL300025497278 none CC(=O)NC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 20, 4, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 28, 94, 94, 94, 94, 94, 1, 30, 30, 30, 30, 20, 20, 20, 20, 4, 1, 1, 1, 1, 1, 18, 18, 94, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 268
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497278 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497278
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497278/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497278
Building REAL300025497279
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497279'
/scratch/stefan/7787277/working/building/REAL300025497279 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497279

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497279/0 /scratch/stefan/7787277/working/building/REAL300025497279 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 132)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/132
`/scratch/stefan/7787277/working/3D/132' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NNC(=O)C=C2)C1)

`REAL300025497279.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497279.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497279/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497279 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NNC(=O)C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 8, 8, 1, 11, 1, 1, 5, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 18, 40, 138, 138, 138, 138, 138, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 17, 1, 18, 18, 138, 1, 1, 1, 1, 1, 5, 17, 17, 17, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37])
total number of confs: 256
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497279 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NNC(=O)C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 8, 8, 1, 11, 1, 1, 5, 7, 7, 6, 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, 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: [44, 17, 44, 76, 114, 201, 201, 201, 201, 201, 17, 17, 17, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 17, 76, 76, 201, 17, 17, 17, 17, 17, 6, 1, 1, 1, 17, 17] 201
rigid atoms, others: [35, 36, 37, 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, 38, 39])
total number of confs: 482
number of broken/clashed sets: 34
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497279 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NNC(=O)C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 8, 8, 1, 11, 1, 1, 5, 7, 7, 6, 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, 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: [99, 46, 13, 1, 1, 1, 1, 1, 1, 1, 99, 138, 138, 138, 138, 138, 200, 200, 200, 201, 201, 201, 201, 201, 201, 138, 46, 46, 1, 138, 138, 138, 138, 138, 200, 201, 201, 201, 138, 138] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 635
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497279 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497279
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497279/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497279
Building REAL300025497280
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497280'
/scratch/stefan/7787277/working/building/REAL300025497280 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497280

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497280/0 /scratch/stefan/7787277/working/building/REAL300025497280 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 133)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/133
`/scratch/stefan/7787277/working/3D/133' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1)

`REAL300025497280.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497280.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497280/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497280 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens 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, 50, 139, 139, 139, 139, 139, 1, 15, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 26, 26, 139, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 40, 23, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 288
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497280 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations 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, 139, 139, 139, 139, 139, 106, 43, 106, 13, 1, 1, 1, 1, 1, 1, 1, 139, 201, 201, 201, 201, 201, 201, 180, 139, 139, 139, 139, 139, 43, 43, 1, 139, 139] 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])
total number of confs: 595
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497280 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
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, 16, 16, 16, 16, 16, 40, 40, 87, 124, 201, 201, 201, 201, 201, 16, 1, 2, 2, 2, 1, 1, 7, 16, 16, 16, 16, 16, 87, 87, 201, 16, 16] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 522
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497280 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497280
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497280/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497280
Building REAL300025497281
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497281'
/scratch/stefan/7787277/working/building/REAL300025497281 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497281

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497281/0 /scratch/stefan/7787277/working/building/REAL300025497281 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 134)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/134
`/scratch/stefan/7787277/working/3D/134' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497281.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497281.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497281/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497281 none O=C(CC1CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 11, 50, 50, 50, 50, 50, 1, 30, 30, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 5, 1, 1, 1, 1, 1, 6, 6, 50, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 243
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497281 none O=C(CC1CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 191, 201, 201, 201, 201, 201, 50, 50, 50, 50, 50, 44, 28, 44, 13, 1, 1, 1, 1, 1, 1, 1, 50, 191, 191, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 91, 50, 50, 50, 50, 50, 28, 28, 1, 50, 50] 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: 774
number of broken/clashed sets: 49
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497281 none O=C(CC1CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 5, 1, 1, 1, 1, 1, 1, 1, 22, 22, 48, 48, 48, 48, 48, 58, 58, 94, 137, 201, 201, 201, 201, 201, 48, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 48, 48, 94, 94, 201, 48, 48] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 37, 35, 36, 38, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 559
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497281 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497281
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497281/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497281
Building REAL300025497282
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497282'
/scratch/stefan/7787277/working/building/REAL300025497282 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497282

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497282/0 /scratch/stefan/7787277/working/building/REAL300025497282 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 135)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/135
`/scratch/stefan/7787277/working/3D/135' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCO2)C1)

`REAL300025497282.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497282.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497282/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497282 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 6, 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]
0  hydrogens 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, 41, 120, 119, 120, 120, 120, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 1, 19, 19, 120, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 12, 12, 1, 1] 201
rigid atoms, others: [1, 40, 41, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 249
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497282 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 6, 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]
0  hydrogens 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, 12, 37, 76, 117, 201, 201, 201, 201, 201, 12, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 12, 76, 76, 201, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 12, 12] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 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, 40, 41])
total number of confs: 492
number of broken/clashed sets: 36
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497282 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 7, 7, 6, 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]
0  hydrogens 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, 43, 13, 1, 1, 1, 1, 1, 1, 1, 85, 120, 120, 120, 120, 120, 186, 186, 186, 201, 201, 201, 201, 120, 43, 43, 1, 120, 120, 120, 120, 120, 186, 201, 201, 201, 201, 201, 201, 201, 120, 120] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 629
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497282 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497282
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497282/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497282
Building REAL300025497283
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497283'
/scratch/stefan/7787277/working/building/REAL300025497283 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497283

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497283/0 /scratch/stefan/7787277/working/building/REAL300025497283 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 136)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/136
`/scratch/stefan/7787277/working/3D/136' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497283.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497283.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497283/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497283 none CSCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 83, 83, 83, 55, 55, 55, 55, 55, 50, 39, 50, 13, 1, 1, 1, 1, 1, 1, 1, 55, 201, 201, 201, 192, 192, 83, 55, 55, 55, 55, 55, 39, 39, 1, 55, 55] 201
rigid atoms, others: [35, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37])
total number of confs: 809
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: REAL300025497283 none CSCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 14, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 26, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 15, 55, 55, 55, 55, 55, 1, 41, 42, 42, 26, 26, 5, 1, 1, 1, 1, 1, 10, 10, 55, 1, 1] 201
rigid atoms, others: [32, 36, 5, 6, 7, 8, 9, 10, 11, 37, 21, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 33, 34, 35])
total number of confs: 211
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497283 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497283
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497283/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497283
Building REAL300025497284
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497284'
/scratch/stefan/7787277/working/building/REAL300025497284 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497284

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497284/0 /scratch/stefan/7787277/working/building/REAL300025497284 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 137)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/137
`/scratch/stefan/7787277/working/3D/137' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1)

`REAL300025497284.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497284.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497284/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497284 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 36, 64, 160, 160, 160, 160, 160, 1, 10, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 37, 37, 160, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 6, 7, 8, 9, 10, 11, 12, 22, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 335
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497284 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 160, 160, 160, 160, 160, 115, 46, 115, 13, 1, 1, 1, 1, 1, 1, 1, 160, 201, 201, 201, 201, 201, 201, 201, 160, 160, 160, 160, 160, 46, 46, 1, 160, 160] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 605
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497284 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 10, 10, 10, 10, 10, 31, 31, 81, 121, 201, 201, 201, 201, 201, 10, 1, 1, 2, 2, 2, 1, 3, 10, 10, 10, 10, 10, 81, 81, 201, 10, 10] 201
rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 509
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497284 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497284
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497284/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497284
Building REAL300025497285
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497285'
/scratch/stefan/7787277/working/building/REAL300025497285 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497285

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497285/0 /scratch/stefan/7787277/working/building/REAL300025497285 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 138)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/138
`/scratch/stefan/7787277/working/3D/138' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497285.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497285.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497285/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497285 none CSCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need 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, 95, 95, 95, 72, 72, 72, 72, 72, 56, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 165, 165, 165, 165, 95, 72, 72, 72, 72, 72, 29, 29, 1, 72, 72] 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])
total number of confs: 727
number of broken/clashed sets: 75
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497285 none CSCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 15, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 14, 72, 72, 72, 72, 72, 1, 32, 32, 32, 15, 15, 13, 13, 4, 1, 1, 1, 1, 1, 7, 7, 72, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 188
number of broken/clashed sets: 75
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497285 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497285
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497285/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497285
Building REAL300025497286
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497286'
/scratch/stefan/7787277/working/building/REAL300025497286 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497286

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497286/0 /scratch/stefan/7787277/working/building/REAL300025497286 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 139)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/139
`/scratch/stefan/7787277/working/3D/139' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497286.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497286.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497286/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497286 none CC(C)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 201, 201, 200, 71, 71, 71, 52, 52, 52, 52, 52, 32, 22, 32, 11, 1, 1, 1, 1, 1, 1, 1, 52, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 71, 52, 52, 52, 52, 52, 22, 22, 1, 52, 52] 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])
total number of confs: 755
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: REAL300025497286 none CC(C)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [28, 28, 28, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 19, 52, 52, 52, 52, 52, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 23, 23, 5, 1, 1, 1, 1, 1, 11, 11, 52, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 201
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497286 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497286
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497286/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497286
Building REAL300025497287
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497287'
/scratch/stefan/7787277/working/building/REAL300025497287 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497287

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497287/0 /scratch/stefan/7787277/working/building/REAL300025497287 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 140)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/140
`/scratch/stefan/7787277/working/3D/140' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC=C2)C1)

`REAL300025497287.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497287.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497287/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497287 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 14, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 1, 12, 12, 91, 1, 1, 1, 1, 1, 4, 13, 13, 13, 1, 1] 201
rigid atoms, others: [1, 36, 37, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34, 35])
total number of confs: 173
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497287 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 14, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 28, 69, 110, 201, 201, 201, 201, 201, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 13, 69, 69, 201, 13, 13, 13, 13, 13, 5, 1, 1, 1, 13, 13] 201
rigid atoms, others: [33, 34, 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, 36, 37])
total number of confs: 499
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497287 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 14, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 37, 13, 1, 1, 1, 1, 1, 1, 1, 69, 91, 91, 91, 91, 91, 121, 121, 121, 201, 201, 201, 201, 91, 37, 37, 1, 91, 91, 91, 91, 91, 121, 201, 201, 201, 91, 91] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 539
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497287 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497287
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497287/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497287
Building REAL300025497288
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497288'
/scratch/stefan/7787277/working/building/REAL300025497288 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497288

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497288/0 /scratch/stefan/7787277/working/building/REAL300025497288 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 141)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/141
`/scratch/stefan/7787277/working/3D/141' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1)

`REAL300025497288.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497288.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497288/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497288 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 7, 7, 7, 6, 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, 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: [18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 28, 100, 100, 100, 100, 100, 1, 17, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 12, 12, 100, 1, 1, 18, 18] 201
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 37, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40])
total number of confs: 193
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497288 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 129, 129, 129, 100, 100, 100, 100, 100, 81, 46, 81, 13, 1, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 201, 201, 129, 100, 100, 100, 100, 100, 46, 46, 1, 100, 100, 201, 201] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 546
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497288 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 18, 18, 34, 34, 66, 111, 201, 201, 201, 201, 201, 18, 1, 1, 1, 2, 2, 2, 7, 18, 18, 18, 18, 18, 66, 66, 201, 18, 18, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 39, 40, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 483
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497288 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497288
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497288/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497288
Building REAL300025497289
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497289'
/scratch/stefan/7787277/working/building/REAL300025497289 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497289

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497289/0 /scratch/stefan/7787277/working/building/REAL300025497289 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 142)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/142
`/scratch/stefan/7787277/working/3D/142' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1C=CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497289.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497289.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497289/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497289 none O=C(CC1C=CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 27, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 19, 67, 67, 67, 67, 67, 1, 27, 27, 52, 52, 52, 52, 52, 52, 52, 4, 1, 1, 1, 1, 1, 11, 11, 67, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 290
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497289 none O=C(CC1C=CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 199, 201, 201, 201, 201, 67, 67, 67, 67, 67, 48, 26, 48, 13, 1, 1, 1, 1, 1, 1, 1, 67, 199, 199, 201, 201, 201, 201, 201, 201, 201, 105, 67, 67, 67, 67, 67, 26, 26, 1, 67, 67] 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])
total number of confs: 752
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497289 none O=C(CC1C=CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 5, 1, 1, 1, 1, 1, 1, 26, 26, 52, 52, 52, 52, 52, 62, 62, 88, 134, 201, 201, 201, 201, 201, 52, 5, 5, 1, 1, 1, 1, 1, 1, 1, 26, 52, 52, 52, 52, 52, 88, 88, 201, 52, 52] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 27, 28, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 519
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497289 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497289
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497289/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497289
Building REAL300025497290
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497290'
/scratch/stefan/7787277/working/building/REAL300025497290 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497290

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497290/0 /scratch/stefan/7787277/working/building/REAL300025497290 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 143)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/143
`/scratch/stefan/7787277/working/3D/143' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1C=NN=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497290.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497290.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497290/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497290 none O=C(CN1C=NN=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 8, 8, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 14, 73, 73, 73, 73, 73, 1, 20, 20, 30, 4, 1, 1, 1, 1, 1, 10, 10, 73, 1, 1] 201
rigid atoms, others: [32, 33, 37, 38, 8, 9, 10, 11, 12, 13, 14, 24, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 34, 35, 36])
total number of confs: 195
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497290 none O=C(CN1C=NN=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 8, 8, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 187, 201, 201, 201, 201, 73, 73, 73, 73, 73, 65, 49, 65, 13, 1, 1, 1, 1, 1, 1, 1, 73, 187, 187, 201, 101, 73, 73, 73, 73, 73, 49, 49, 1, 73, 73] 201
rigid atoms, others: [36, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 782
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497290 none O=C(CN1C=NN=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 8, 8, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 19, 19, 30, 30, 30, 30, 30, 47, 47, 86, 119, 201, 201, 201, 201, 201, 30, 6, 6, 1, 19, 30, 30, 30, 30, 30, 86, 86, 201, 30, 30] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 561
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497290 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497290
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497290/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497290
Building REAL300025497291
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497291'
/scratch/stefan/7787277/working/building/REAL300025497291 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497291

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497291/0 /scratch/stefan/7787277/working/building/REAL300025497291 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 144)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/144
`/scratch/stefan/7787277/working/3D/144' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1CCCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497291.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497291.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497291/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497291 none O=C(CN1CCCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 26, 93, 93, 93, 93, 93, 1, 20, 20, 31, 31, 31, 31, 31, 31, 4, 1, 1, 1, 1, 1, 15, 15, 93, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 244
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497291 none O=C(CN1CCCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 200, 201, 201, 201, 201, 201, 93, 93, 93, 93, 93, 53, 30, 53, 13, 1, 1, 1, 1, 1, 1, 1, 93, 200, 200, 201, 201, 201, 201, 201, 201, 113, 93, 93, 93, 93, 93, 30, 30, 1, 93, 93] 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])
total number of confs: 748
number of broken/clashed sets: 59
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497291 none O=C(CN1CCCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 18, 18, 31, 31, 31, 31, 31, 52, 52, 83, 125, 201, 201, 201, 201, 201, 31, 6, 6, 1, 1, 1, 1, 1, 1, 18, 31, 31, 31, 31, 31, 83, 83, 201, 31, 31] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 533
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497291 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497291
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497291/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497291
Building REAL300025497292
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497292'
/scratch/stefan/7787277/working/building/REAL300025497292 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497292

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497292/0 /scratch/stefan/7787277/working/building/REAL300025497292 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 145)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/145
`/scratch/stefan/7787277/working/3D/145' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1)

`REAL300025497292.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497292.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497292/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497292 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 54, 145, 144, 145, 145, 145, 1, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 21, 21, 145, 1, 1, 13] 201
rigid atoms, others: [32, 33, 34, 38, 6, 7, 8, 9, 10, 11, 12, 22, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40])
total number of confs: 277
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497292 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 184, 184, 184, 145, 145, 145, 145, 145, 128, 59, 128, 13, 1, 1, 1, 1, 1, 1, 1, 145, 201, 201, 201, 201, 201, 201, 184, 145, 145, 145, 145, 145, 59, 59, 1, 145, 145, 201] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 607
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497292 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 13, 13, 13, 13, 13, 35, 35, 67, 118, 201, 201, 201, 201, 201, 13, 1, 1, 2, 2, 2, 1, 5, 13, 13, 13, 13, 13, 67, 67, 201, 13, 13, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 40, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 462
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497292 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497292
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497292/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497292
Building REAL300025497293
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497293'
/scratch/stefan/7787277/working/building/REAL300025497293 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497293

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497293/0 /scratch/stefan/7787277/working/building/REAL300025497293 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 146)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/146
`/scratch/stefan/7787277/working/3D/146' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497293.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497293.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497293/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497293 none CC1=NOC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 23, 72, 72, 72, 72, 72, 1, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 13, 13, 72, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 158
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497293 none CC1=NOC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 89, 89, 89, 72, 72, 72, 72, 72, 59, 39, 59, 13, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 201, 201, 89, 72, 72, 72, 72, 72, 39, 39, 1, 72, 72] 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])
total number of confs: 461
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497293 none CC1=NOC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 21, 21, 21, 21, 21, 39, 39, 67, 99, 201, 201, 201, 201, 201, 21, 2, 2, 2, 2, 2, 2, 9, 21, 21, 21, 21, 21, 67, 67, 201, 21, 21] 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])
total number of confs: 497
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497293 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497293
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497293/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497293
Building REAL300025497294
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497294'
/scratch/stefan/7787277/working/building/REAL300025497294 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497294

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497294/0 /scratch/stefan/7787277/working/building/REAL300025497294 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 147)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/147
`/scratch/stefan/7787277/working/3D/147' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SN=N1)

`REAL300025497294.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497294.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497294/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497294 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 30, 107, 107, 107, 107, 107, 1, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 13, 13, 107, 1, 1] 201
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 37, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36])
total number of confs: 200
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497294 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 132, 132, 132, 107, 107, 107, 107, 107, 91, 47, 91, 13, 1, 1, 1, 1, 1, 1, 1, 107, 201, 201, 201, 201, 201, 201, 132, 107, 107, 107, 107, 107, 47, 47, 1, 107, 107] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 552
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497294 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 16, 16, 16, 16, 16, 36, 36, 71, 116, 201, 201, 201, 201, 201, 16, 1, 1, 1, 2, 2, 2, 7, 16, 16, 16, 16, 16, 71, 71, 201, 16, 16] 201
rigid atoms, others: [0, 1, 2, 3, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 499
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497294 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497294
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497294/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497294
Building REAL300025497295
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497295'
/scratch/stefan/7787277/working/building/REAL300025497295 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497295

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497295/0 /scratch/stefan/7787277/working/building/REAL300025497295 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 148)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/148
`/scratch/stefan/7787277/working/3D/148' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1)

`REAL300025497295.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497295.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497295/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497295 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 53, 134, 134, 134, 134, 134, 1, 19, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 27, 27, 134, 1, 1, 19, 19, 19] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43])
total number of confs: 281
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497295 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 179, 179, 179, 134, 134, 134, 134, 134, 107, 44, 107, 13, 1, 1, 1, 1, 1, 1, 1, 134, 201, 201, 201, 201, 201, 201, 201, 179, 134, 134, 134, 134, 134, 44, 44, 1, 134, 134, 201, 201, 201] 201
rigid atoms, others: [38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43])
total number of confs: 584
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497295 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 19, 19, 19, 19, 19, 45, 45, 106, 138, 201, 201, 201, 201, 201, 19, 1, 1, 1, 2, 2, 2, 1, 9, 19, 19, 19, 19, 19, 106, 106, 201, 19, 19, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 569
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497295 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497295
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497295/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497295
Building REAL300025497296
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497296'
/scratch/stefan/7787277/working/building/REAL300025497296 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497296

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497296/0 /scratch/stefan/7787277/working/building/REAL300025497296 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 149)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/149
`/scratch/stefan/7787277/working/3D/149' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC=CCC2)C1)

`REAL300025497296.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497296.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497296/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497296 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC=CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 20, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 1, 13, 13, 74, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 43, 44, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 171
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497296 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC=CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 18, 42, 79, 110, 201, 201, 201, 201, 201, 18, 18, 18, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 79, 79, 201, 18, 18, 18, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [34, 35, 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, 43, 44])
total number of confs: 512
number of broken/clashed sets: 24
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497296 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC=CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 37, 13, 1, 1, 1, 1, 1, 1, 1, 56, 74, 74, 74, 74, 74, 104, 104, 104, 201, 201, 201, 201, 201, 74, 37, 37, 1, 74, 74, 74, 74, 74, 104, 201, 201, 201, 201, 201, 201, 201, 201, 201, 74, 74] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 650
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497296 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497296
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497296/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497296
Building REAL300025497297
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497297'
/scratch/stefan/7787277/working/building/REAL300025497297 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497297

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497297/0 /scratch/stefan/7787277/working/building/REAL300025497297 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 150)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/150
`/scratch/stefan/7787277/working/3D/150' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497297.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497297.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497297/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497297 none CC1=NOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 35, 62, 157, 157, 157, 157, 157, 1, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 35, 35, 157, 1, 1, 12] 201
rigid atoms, others: [32, 33, 37, 38, 7, 8, 9, 10, 11, 12, 13, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 34, 35, 36, 39])
total number of confs: 327
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497297 none CC1=NOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 157, 157, 157, 157, 157, 111, 46, 111, 13, 1, 1, 1, 1, 1, 1, 1, 157, 201, 201, 201, 201, 196, 157, 157, 157, 157, 157, 46, 46, 1, 157, 157, 201] 201
rigid atoms, others: [36, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39])
total number of confs: 603
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497297 none CC1=NOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 12, 12, 12, 12, 12, 35, 35, 89, 127, 201, 201, 201, 201, 201, 12, 1, 2, 2, 2, 4, 12, 12, 12, 12, 12, 89, 89, 201, 12, 12, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 527
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497297 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497297
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497297/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497297
Building REAL300025497298
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497298'
/scratch/stefan/7787277/working/building/REAL300025497298 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497298

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497298/0 /scratch/stefan/7787277/working/building/REAL300025497298 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 151)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/151
`/scratch/stefan/7787277/working/3D/151' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN2)C1)

`REAL300025497298.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497298.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497298/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497298 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 22, 49, 134, 134, 134, 134, 134, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 1, 22, 22, 134, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 1, 1] 201
rigid atoms, others: [1, 37, 38, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34, 35, 36])
total number of confs: 257
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497298 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 13, 32, 69, 116, 201, 201, 201, 201, 201, 13, 13, 13, 13, 6, 6, 1, 6, 1, 1, 1, 1, 1, 13, 69, 69, 201, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 13, 13] 201
rigid atoms, others: [33, 34, 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, 37, 38])
total number of confs: 472
number of broken/clashed sets: 35
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497298 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 48, 13, 1, 1, 1, 1, 1, 1, 1, 102, 134, 134, 134, 134, 134, 186, 186, 186, 201, 201, 201, 201, 134, 48, 48, 1, 134, 134, 134, 134, 134, 186, 201, 201, 201, 201, 134, 134] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 608
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497298 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497298
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497298/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497298
Building REAL300025497299
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497299'
/scratch/stefan/7787277/working/building/REAL300025497299 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497299

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497299/0 /scratch/stefan/7787277/working/building/REAL300025497299 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 152)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/152
`/scratch/stefan/7787277/working/3D/152' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(Cl)=CN2)C1)

`REAL300025497299.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497299.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497299/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497299 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(Cl)=CN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 16, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 41, 123, 123, 123, 123, 123, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 18, 18, 123, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1] 201
rigid atoms, others: [32, 1, 37, 38, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36])
total number of confs: 237
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497299 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(Cl)=CN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 16, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 15, 37, 76, 117, 201, 201, 201, 201, 201, 15, 15, 15, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 15, 76, 76, 201, 15, 15, 15, 15, 15, 8, 1, 1, 1, 15, 15] 201
rigid atoms, others: [34, 35, 36, 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, 37, 38])
total number of confs: 492
number of broken/clashed sets: 33
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497299 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(Cl)=CN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'N.pl3', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 16, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 46, 13, 1, 1, 1, 1, 1, 1, 1, 94, 123, 123, 123, 123, 123, 187, 187, 187, 201, 201, 201, 201, 201, 123, 46, 46, 1, 123, 123, 123, 123, 123, 187, 201, 201, 201, 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: 619
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497299 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497299
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497299/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497299
Building REAL300025497300
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497300'
/scratch/stefan/7787277/working/building/REAL300025497300 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497300

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497300/0 /scratch/stefan/7787277/working/building/REAL300025497300 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 153)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/153
`/scratch/stefan/7787277/working/3D/153' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497300.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497300.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497300/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497300 none CC(=O)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 150, 159, 57, 57, 57, 54, 54, 54, 54, 54, 44, 28, 44, 13, 1, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 189, 198, 177, 177, 159, 159, 57, 54, 54, 54, 54, 54, 28, 28, 1, 54, 54] 201
rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44])
total number of confs: 987
number of broken/clashed sets: 155
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497300 none CC(=O)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 16, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 18, 54, 54, 54, 54, 54, 1, 44, 44, 44, 32, 35, 20, 20, 12, 12, 3, 1, 1, 1, 1, 1, 10, 10, 54, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 298
number of broken/clashed sets: 155
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497300 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497300
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497300/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497300
Building REAL300025497301
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497301'
/scratch/stefan/7787277/working/building/REAL300025497301 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497301

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497301/0 /scratch/stefan/7787277/working/building/REAL300025497301 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 154)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/154
`/scratch/stefan/7787277/working/3D/154' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N1C)

`REAL300025497301.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497301.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497301/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497301 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.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, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 38, 103, 103, 103, 103, 103, 1, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 22, 22, 103, 1, 1, 15, 15, 15] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44])
total number of confs: 225
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497301 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.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, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 136, 136, 136, 103, 103, 103, 103, 103, 81, 38, 81, 13, 1, 1, 1, 1, 1, 1, 1, 103, 201, 201, 201, 201, 201, 201, 201, 136, 103, 103, 103, 103, 103, 38, 38, 1, 103, 103, 201, 201, 201] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44])
total number of confs: 563
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497301 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.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, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 15, 15, 15, 15, 15, 41, 41, 90, 128, 201, 201, 201, 201, 201, 15, 1, 1, 2, 2, 2, 1, 1, 6, 15, 15, 15, 15, 15, 90, 90, 201, 15, 15, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 555
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497301 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497301
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497301/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497301
Building REAL300025497302
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497302'
/scratch/stefan/7787277/working/building/REAL300025497302 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497302

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497302/0 /scratch/stefan/7787277/working/building/REAL300025497302 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 155)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/155
`/scratch/stefan/7787277/working/3D/155' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COC=C2)C1)

`REAL300025497302.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497302.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497302/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497302 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 14, 27, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 1, 14, 14, 94, 1, 1, 1, 1, 1, 5, 14, 14, 14, 1, 1] 201
rigid atoms, others: [1, 36, 37, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34, 35])
total number of confs: 188
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497302 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 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, 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: [39, 14, 39, 82, 120, 201, 201, 201, 201, 201, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 14, 82, 82, 201, 14, 14, 14, 14, 14, 5, 1, 1, 1, 14, 14] 201
rigid atoms, others: [33, 34, 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, 36, 37])
total number of confs: 529
number of broken/clashed sets: 24
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497302 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 12, 1, 1, 5, 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, 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: [60, 39, 13, 1, 1, 1, 1, 1, 1, 1, 60, 94, 94, 94, 94, 94, 136, 136, 136, 201, 201, 201, 201, 94, 39, 39, 1, 94, 94, 94, 94, 94, 136, 201, 201, 201, 94, 94] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 540
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497302 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497302
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497302/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497302
Building REAL300025497303
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497303'
/scratch/stefan/7787277/working/building/REAL300025497303 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497303

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497303/0 /scratch/stefan/7787277/working/building/REAL300025497303 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 156)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/156
`/scratch/stefan/7787277/working/3D/156' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1C=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497303.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497303.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497303/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497303 none O=C(CN1C=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 20, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 23, 88, 88, 88, 88, 88, 1, 20, 20, 28, 28, 28, 5, 1, 1, 1, 1, 1, 13, 13, 88, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 230
number of broken/clashed sets: 57
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497303 none O=C(CN1C=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 201, 201, 201, 201, 201, 88, 88, 88, 88, 88, 54, 30, 54, 13, 1, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 201, 201, 125, 88, 88, 88, 88, 88, 30, 30, 1, 88, 88] 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])
total number of confs: 790
number of broken/clashed sets: 57
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497303 none O=C(CN1C=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 7, 1, 1, 1, 1, 1, 1, 16, 16, 28, 28, 28, 28, 28, 47, 47, 81, 120, 201, 201, 201, 201, 201, 28, 7, 7, 1, 1, 1, 16, 28, 28, 28, 28, 28, 81, 81, 201, 28, 28] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 537
number of broken/clashed sets: 57
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497303 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497303
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497303/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497303
Building REAL300025497304
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497304'
/scratch/stefan/7787277/working/building/REAL300025497304 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497304

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497304/0 /scratch/stefan/7787277/working/building/REAL300025497304 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 157)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/157
`/scratch/stefan/7787277/working/3D/157' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)OC=C1)

`REAL300025497304.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497304.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497304/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497304 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)OC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 1, 7, 7, 7, 6, 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, 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 35, 130, 130, 130, 130, 130, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 13, 13, 130, 1, 1, 11, 11] 201
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 37, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40])
total number of confs: 222
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497304 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)OC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 1, 7, 7, 7, 6, 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, 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, 166, 166, 166, 130, 130, 130, 130, 130, 105, 45, 105, 13, 1, 1, 1, 1, 1, 1, 1, 130, 201, 201, 201, 201, 201, 201, 166, 130, 130, 130, 130, 130, 45, 45, 1, 130, 130, 201, 201] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 572
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497304 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)OC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 1, 7, 7, 7, 6, 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, 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, 4, 4, 4, 11, 11, 11, 11, 11, 30, 30, 69, 122, 201, 201, 201, 201, 201, 11, 1, 1, 1, 2, 2, 2, 4, 11, 11, 11, 11, 11, 69, 69, 201, 11, 11, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 39, 40, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 503
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497304 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497304
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497304/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497304
Building REAL300025497305
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497305'
/scratch/stefan/7787277/working/building/REAL300025497305 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497305

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497305/0 /scratch/stefan/7787277/working/building/REAL300025497305 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 158)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/158
`/scratch/stefan/7787277/working/3D/158' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3CCC2C3)C1)

`REAL300025497305.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497305.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497305/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497305 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3CCC2C3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 20, 46, 170, 169, 170, 170, 170, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 7, 1, 21, 21, 170, 1, 1, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 201
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 14, 15, 46, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 298
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497305 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3CCC2C3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 51, 97, 201, 201, 201, 201, 201, 7, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 7, 51, 51, 201, 7, 7, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 201
rigid atoms, others: [35, 36, 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, 46, 47])
total number of confs: 429
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497305 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3CCC2C3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [128, 61, 13, 1, 1, 1, 1, 1, 1, 1, 128, 170, 170, 170, 170, 170, 199, 199, 199, 201, 201, 201, 201, 201, 201, 170, 61, 61, 1, 170, 170, 170, 170, 170, 199, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 170, 170] 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: 590
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497305 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497305
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497305/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497305
Building REAL300025497306
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497306'
/scratch/stefan/7787277/working/building/REAL300025497306 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497306

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497306/0 /scratch/stefan/7787277/working/building/REAL300025497306 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 159)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/159
`/scratch/stefan/7787277/working/3D/159' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(Cl)O2)C1)

`REAL300025497306.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497306.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497306/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497306 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(Cl)O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 16, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 47, 129, 129, 129, 129, 129, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 21, 21, 129, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 36, 37, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35])
total number of confs: 246
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497306 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(Cl)O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 16, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 25, 60, 99, 201, 201, 201, 201, 201, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 60, 60, 201, 8, 8, 8, 8, 8, 3, 1, 1, 8, 8] 201
rigid atoms, others: [34, 35, 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, 36, 37])
total number of confs: 446
number of broken/clashed sets: 31
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497306 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(Cl)O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 16, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 38, 13, 1, 1, 1, 1, 1, 1, 1, 94, 129, 129, 129, 129, 129, 198, 198, 198, 201, 201, 201, 201, 201, 129, 38, 38, 1, 129, 129, 129, 129, 129, 198, 201, 201, 129, 129] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 617
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497306 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497306
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497306/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497306
Building REAL300025497307
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497307'
/scratch/stefan/7787277/working/building/REAL300025497307 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497307

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497307/0 /scratch/stefan/7787277/working/building/REAL300025497307 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 160)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/160
`/scratch/stefan/7787277/working/3D/160' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C)

`REAL300025497307.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497307.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497307/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497307 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 5, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 33, 74, 74, 74, 74, 74, 1, 20, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 20, 20, 74, 1, 1, 20, 20, 20, 20] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 21, 39, 38, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43])
total number of confs: 188
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497307 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 5, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 95, 95, 95, 74, 74, 74, 74, 74, 61, 38, 61, 13, 1, 1, 1, 1, 1, 1, 1, 74, 201, 201, 201, 201, 201, 201, 201, 95, 74, 74, 74, 74, 74, 38, 38, 1, 74, 74, 201, 201, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 473
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497307 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 5, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 20, 20, 20, 20, 20, 52, 52, 99, 140, 201, 201, 201, 201, 201, 20, 1, 1, 1, 1, 2, 2, 2, 8, 20, 20, 20, 20, 20, 99, 99, 201, 20, 20, 1, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 40, 22, 23, 24, 25] set([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, 41, 42, 43])
total number of confs: 570
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497307 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497307
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497307/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497307
Building REAL300025497308
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497308'
/scratch/stefan/7787277/working/building/REAL300025497308 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497308

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497308/0 /scratch/stefan/7787277/working/building/REAL300025497308 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 161)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/161
`/scratch/stefan/7787277/working/3D/161' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497308.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497308.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497308/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497308 none CCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 201, 201, 190, 88, 88, 88, 47, 47, 47, 47, 47, 43, 29, 43, 13, 1, 1, 1, 1, 1, 1, 1, 47, 201, 201, 201, 201, 201, 201, 201, 201, 201, 190, 190, 88, 47, 47, 47, 47, 47, 29, 29, 1, 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])
total number of confs: 788
number of broken/clashed sets: 56
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497308 none CCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [35, 41, 35, 27, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 11, 47, 47, 47, 47, 47, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 27, 27, 5, 1, 1, 1, 1, 1, 6, 6, 47, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 310
number of broken/clashed sets: 56
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497308 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497308
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497308/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497308
Building REAL300025497309
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497309'
/scratch/stefan/7787277/working/building/REAL300025497309 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497309

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497309/0 /scratch/stefan/7787277/working/building/REAL300025497309 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 162)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/162
`/scratch/stefan/7787277/working/3D/162' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497309.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497309.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497309/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497309 none CC(C)(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 201, 201, 201, 119, 119, 119, 81, 81, 81, 81, 81, 68, 42, 68, 13, 1, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 81, 81, 81, 81, 81, 42, 42, 1, 81, 81] 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])
total number of confs: 884
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: REAL300025497309 none CC(C)(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [10, 9, 10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 28, 81, 81, 81, 81, 81, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 9, 5, 1, 1, 1, 1, 1, 13, 13, 81, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 185
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497309 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497309
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497309/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497309
Building REAL300025497310
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497310'
/scratch/stefan/7787277/working/building/REAL300025497310 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497310

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497310/0 /scratch/stefan/7787277/working/building/REAL300025497310 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 163)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/163
`/scratch/stefan/7787277/working/3D/163' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1)

`REAL300025497310.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497310.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497310/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497310 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 33, 111, 111, 111, 111, 111, 1, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 16, 16, 111, 1, 1, 14] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42])
total number of confs: 213
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497310 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 153, 153, 153, 111, 111, 111, 111, 111, 88, 48, 88, 13, 1, 1, 1, 1, 1, 1, 1, 111, 201, 201, 201, 201, 201, 201, 201, 153, 111, 111, 111, 111, 111, 48, 48, 1, 111, 111, 201] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42])
total number of confs: 573
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497310 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 14, 14, 14, 14, 14, 38, 38, 75, 119, 201, 201, 201, 201, 201, 14, 1, 1, 2, 2, 2, 1, 1, 5, 14, 14, 14, 14, 14, 75, 75, 201, 14, 14, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 507
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497310 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497310
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497310/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497310
Building REAL300025497311
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497311'
/scratch/stefan/7787277/working/building/REAL300025497311 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497311

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497311/0 /scratch/stefan/7787277/working/building/REAL300025497311 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 164)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/164
`/scratch/stefan/7787277/working/3D/164' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497311.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497311.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497311/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497311 none CN1C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 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: [12, 12, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 48, 146, 146, 146, 146, 146, 1, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 17, 17, 146, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 259
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497311 none CN1C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 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, 199, 199, 199, 146, 146, 146, 146, 146, 123, 50, 123, 13, 1, 1, 1, 1, 1, 1, 1, 146, 201, 201, 201, 201, 201, 201, 199, 146, 146, 146, 146, 146, 50, 50, 1, 146, 146] 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])
total number of confs: 602
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497311 none CN1C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 26, 26, 62, 113, 201, 201, 201, 201, 201, 12, 2, 2, 2, 1, 1, 1, 4, 12, 12, 12, 12, 12, 62, 62, 201, 12, 12] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 471
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497311 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497311
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497311/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497311
Building REAL300025497312
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497312'
/scratch/stefan/7787277/working/building/REAL300025497312 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497312

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497312/0 /scratch/stefan/7787277/working/building/REAL300025497312 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 165)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/165
`/scratch/stefan/7787277/working/3D/165' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCN1C=NC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497312.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497312.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497312/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497312 none O=C(CCN1C=NC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 8, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 17, 21, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 24, 78, 78, 78, 78, 78, 1, 17, 17, 21, 21, 32, 32, 5, 1, 1, 1, 1, 1, 15, 15, 78, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 241
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497312 none O=C(CCN1C=NC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 8, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 104, 196, 200, 201, 201, 201, 201, 78, 78, 78, 78, 78, 43, 28, 43, 13, 1, 1, 1, 1, 1, 1, 1, 78, 196, 196, 200, 200, 201, 201, 104, 78, 78, 78, 78, 78, 28, 28, 1, 78, 78] 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])
total number of confs: 752
number of broken/clashed sets: 43
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497312 none O=C(CCN1C=NC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 8, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 22, 22, 32, 32, 32, 32, 32, 54, 54, 88, 122, 201, 201, 201, 201, 201, 32, 9, 9, 5, 5, 1, 1, 22, 32, 32, 32, 32, 32, 88, 88, 201, 32, 32] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 562
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497312 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497312
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497312/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497312
Building REAL300025497313
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497313'
/scratch/stefan/7787277/working/building/REAL300025497313 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497313

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497313/0 /scratch/stefan/7787277/working/building/REAL300025497313 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 166)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/166
`/scratch/stefan/7787277/working/3D/166' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497313.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497313.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497313/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497313 none CCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 195, 71, 71, 71, 40, 40, 40, 40, 40, 34, 22, 34, 12, 1, 1, 1, 1, 1, 1, 1, 40, 201, 201, 201, 201, 201, 201, 201, 195, 195, 71, 40, 40, 40, 40, 40, 22, 22, 1, 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])
total number of confs: 761
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: REAL300025497313 none CCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [38, 31, 24, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 11, 40, 40, 40, 40, 40, 1, 38, 38, 38, 38, 38, 38, 38, 24, 24, 5, 1, 1, 1, 1, 1, 6, 6, 40, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 267
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497313 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497313
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497313/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497313
Building REAL300025497314
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497314'
/scratch/stefan/7787277/working/building/REAL300025497314 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497314

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497314/0 /scratch/stefan/7787277/working/building/REAL300025497314 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 167)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/167
`/scratch/stefan/7787277/working/3D/167' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025497314.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497314.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497314/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497314 none CC1=CC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 31, 54, 148, 148, 148, 148, 148, 1, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 31, 31, 148, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 303
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497314 none CC1=CC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
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, 148, 148, 148, 148, 148, 106, 42, 106, 13, 1, 1, 1, 1, 1, 1, 1, 148, 201, 201, 201, 201, 201, 201, 201, 201, 148, 148, 148, 148, 148, 42, 42, 1, 148, 148] 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])
total number of confs: 595
number of broken/clashed sets: 29
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497314 none CC1=CC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 9, 9, 9, 9, 9, 27, 27, 78, 114, 201, 201, 201, 201, 201, 9, 1, 2, 2, 2, 1, 1, 1, 3, 9, 9, 9, 9, 9, 78, 78, 201, 9, 9] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 512
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497314 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497314
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497314/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497314
Building REAL300025497315
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497315'
/scratch/stefan/7787277/working/building/REAL300025497315 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497315

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497315/0 /scratch/stefan/7787277/working/building/REAL300025497315 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 168)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/168
`/scratch/stefan/7787277/working/3D/168' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497315.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497315.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497315/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497315 none CC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need 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, 201, 155, 155, 109, 109, 109, 109, 109, 95, 52, 95, 13, 1, 1, 1, 1, 1, 1, 1, 109, 201, 201, 201, 201, 201, 201, 201, 155, 109, 109, 109, 109, 109, 52, 52, 1, 109, 109] 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])
total number of confs: 781
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: REAL300025497315 none CC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 4, 15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 29, 109, 109, 109, 109, 109, 1, 15, 15, 15, 15, 15, 15, 15, 4, 1, 1, 1, 1, 1, 14, 14, 109, 1, 1] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 21, 39, 38, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 221
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497315 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497315
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497315/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497315
Building REAL300025497316
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497316'
/scratch/stefan/7787277/working/building/REAL300025497316 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497316

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497316/0 /scratch/stefan/7787277/working/building/REAL300025497316 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 169)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/169
`/scratch/stefan/7787277/working/3D/169' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCN1C=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497316.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497316.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497316/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497316 none O=C(CCN1C=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 16, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 28, 97, 97, 97, 97, 97, 1, 14, 14, 16, 16, 21, 21, 21, 5, 1, 1, 1, 1, 1, 16, 16, 97, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 239
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497316 none O=C(CCN1C=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 195, 196, 201, 201, 201, 201, 97, 97, 97, 97, 97, 58, 29, 58, 13, 1, 1, 1, 1, 1, 1, 1, 97, 195, 195, 196, 196, 201, 201, 201, 125, 97, 97, 97, 97, 97, 29, 29, 1, 97, 97] 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])
total number of confs: 726
number of broken/clashed sets: 43
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497316 none O=C(CCN1C=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 21, 21, 21, 21, 21, 40, 40, 78, 117, 201, 201, 201, 201, 201, 21, 8, 8, 5, 5, 1, 1, 1, 14, 21, 21, 21, 21, 21, 78, 78, 201, 21, 21] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 542
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497316 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497316
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497316/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497316
Building REAL300025497317
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497317'
/scratch/stefan/7787277/working/building/REAL300025497317 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497317

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497317/0 /scratch/stefan/7787277/working/building/REAL300025497317 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 170)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/170
`/scratch/stefan/7787277/working/3D/170' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC=C2O)C1)

`REAL300025497317.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497317.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497317/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497317 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC=C2O)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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]
1  hydrogens need rotated
402  conformations in input
total number of sets (complete confs): 402
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 16, 31, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 9, 10, 10, 10, 1, 16, 16, 93, 1, 1, 1, 1, 1, 5, 10, 10, 10, 10, 20, 1, 1] 402
rigid atoms, others: [32, 1, 33, 40, 41, 10, 11, 12, 13, 14, 15, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39])
total number of confs: 214
number of broken/clashed sets: 142
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497317 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC=C2O)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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]
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: [30, 10, 30, 65, 98, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 10, 65, 65, 201, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 2, 10, 10] 402
rigid atoms, others: [35, 36, 37, 38, 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, 39, 40, 41])
total number of confs: 469
number of broken/clashed sets: 142
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497317 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC=C2O)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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]
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: [64, 36, 12, 1, 1, 1, 1, 1, 1, 1, 64, 93, 93, 93, 93, 93, 136, 136, 136, 201, 201, 201, 201, 201, 201, 93, 36, 36, 1, 93, 93, 93, 93, 93, 136, 201, 201, 201, 201, 402, 93, 93] 402
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 954
number of broken/clashed sets: 142
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497317 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497317
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497317/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497317
Building REAL300025497318
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497318'
/scratch/stefan/7787277/working/building/REAL300025497318 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497318

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497318/0 /scratch/stefan/7787277/working/building/REAL300025497318 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 171)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/171
`/scratch/stefan/7787277/working/3D/171' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497318.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497318.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497318/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497318 none CCC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 116, 201, 116, 116, 77, 77, 77, 77, 77, 61, 44, 61, 13, 1, 1, 1, 1, 1, 1, 1, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 116, 77, 77, 77, 77, 77, 44, 44, 1, 77, 77] 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])
total number of confs: 811
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: REAL300025497318 none CCC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [22, 19, 5, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 24, 77, 77, 77, 77, 77, 1, 22, 22, 22, 22, 22, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 11, 11, 77, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 214
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497318 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497318
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497318/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497318
Building REAL300025497319
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497319'
/scratch/stefan/7787277/working/building/REAL300025497319 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497319

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497319/0 /scratch/stefan/7787277/working/building/REAL300025497319 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 172)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/172
`/scratch/stefan/7787277/working/3D/172' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)SCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497319.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497319.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497319/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497319 none CC(C)SCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 198, 201, 187, 95, 95, 95, 85, 85, 85, 85, 85, 60, 29, 60, 13, 1, 1, 1, 1, 1, 1, 1, 85, 201, 201, 201, 201, 201, 201, 201, 187, 187, 95, 85, 85, 85, 85, 85, 29, 29, 1, 85, 85] 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])
total number of confs: 740
number of broken/clashed sets: 98
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497319 none CC(C)SCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [25, 19, 25, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 17, 85, 85, 85, 85, 85, 1, 25, 25, 25, 25, 25, 25, 25, 10, 10, 3, 1, 1, 1, 1, 1, 8, 8, 85, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 212
number of broken/clashed sets: 98
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497319 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497319
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497319/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497319
Building REAL300025497320
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497320'
/scratch/stefan/7787277/working/building/REAL300025497320 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497320

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497320/0 /scratch/stefan/7787277/working/building/REAL300025497320 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 173)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/173
`/scratch/stefan/7787277/working/3D/173' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497320.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497320.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497320/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497320 none CC(=O)N(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 200, 201, 135, 135, 135, 108, 108, 108, 108, 108, 62, 30, 62, 13, 1, 1, 1, 1, 1, 1, 1, 108, 201, 201, 201, 201, 201, 201, 200, 200, 135, 108, 108, 108, 108, 108, 30, 30, 1, 108, 108] 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])
total number of confs: 710
number of broken/clashed sets: 51
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497320 none CC(=O)N(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 21, 28, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 30, 108, 108, 108, 108, 108, 1, 28, 28, 28, 28, 28, 28, 21, 21, 4, 1, 1, 1, 1, 1, 16, 16, 108, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 278
number of broken/clashed sets: 51
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497320 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497320
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497320/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497320
Building REAL300025497321
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497321'
/scratch/stefan/7787277/working/building/REAL300025497321 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497321

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497321/0 /scratch/stefan/7787277/working/building/REAL300025497321 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 174)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/174
`/scratch/stefan/7787277/working/3D/174' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497321.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497321.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497321/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497321 none CCC(CC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [16, 15, 14, 15, 16, 14, 14, 11, 11, 11, 11, 11, 11, 11, 11, 9, 1, 1, 1, 1, 1, 1, 1, 11, 16, 16, 16, 16, 16, 15, 16, 16, 16, 16, 16, 14, 11, 11, 11, 11, 11, 11, 11, 1, 11, 11] 16
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])
total number of confs: 50
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: REAL300025497321 none CCC(CC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [10, 8, 4, 8, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 11, 11, 11, 11, 11, 1, 10, 10, 10, 10, 10, 8, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 6, 6, 11, 1, 1] 16
rigid atoms, others: [45, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 79
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497321 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497321
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497321/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497321
Building REAL300025497322
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497322'
/scratch/stefan/7787277/working/building/REAL300025497322 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497322

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497322/0 /scratch/stefan/7787277/working/building/REAL300025497322 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 175)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/175
`/scratch/stefan/7787277/working/3D/175' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497322.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497322.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497322/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497322 none CC(C)OCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 154, 201, 140, 139, 71, 71, 71, 62, 62, 62, 62, 62, 47, 28, 47, 13, 1, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 201, 201, 201, 140, 140, 139, 139, 71, 62, 62, 62, 62, 62, 28, 28, 1, 62, 62] 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])
total number of confs: 859
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: REAL300025497322 none CC(C)OCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 14, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 13, 62, 62, 62, 62, 62, 1, 32, 32, 32, 32, 32, 32, 32, 14, 14, 12, 12, 3, 1, 1, 1, 1, 1, 7, 7, 62, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 230
number of broken/clashed sets: 105
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497322 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497322
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497322/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497322
Building REAL300025497323
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497323'
/scratch/stefan/7787277/working/building/REAL300025497323 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497323

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497323/0 /scratch/stefan/7787277/working/building/REAL300025497323 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 176)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/176
`/scratch/stefan/7787277/working/3D/176' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497323.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497323.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497323/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497323 none CCC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 7, 7, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 34, 89, 89, 89, 89, 89, 1, 7, 17, 17, 17, 17, 17, 7, 5, 1, 1, 1, 1, 1, 19, 19, 89, 1, 1, 7] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 241
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497323 none CCC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 117, 117, 117, 117, 115, 115, 115, 89, 89, 89, 89, 89, 72, 38, 72, 13, 1, 1, 1, 1, 1, 1, 1, 89, 117, 201, 201, 201, 201, 201, 117, 115, 89, 89, 89, 89, 89, 38, 38, 1, 89, 89, 117] 201
rigid atoms, others: [40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43])
total number of confs: 881
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497323 none CCC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 7, 7, 7, 7, 7, 20, 20, 41, 61, 117, 117, 117, 117, 117, 7, 1, 6, 6, 6, 6, 6, 1, 4, 7, 7, 7, 7, 7, 41, 41, 117, 7, 7, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 43, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 299
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497323 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497323
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497323/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497323
Building REAL300025497324
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497324'
/scratch/stefan/7787277/working/building/REAL300025497324 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497324

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497324/0 /scratch/stefan/7787277/working/building/REAL300025497324 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 177)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/177
`/scratch/stefan/7787277/working/3D/177' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1CCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497324.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497324.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497324/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497324 none O=C(CCC1CCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 22, 25, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 16, 70, 70, 70, 70, 70, 1, 22, 22, 26, 26, 31, 31, 31, 31, 31, 31, 31, 5, 1, 1, 1, 1, 1, 8, 8, 70, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 228
number of broken/clashed sets: 70
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497324 none O=C(CCC1CCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 197, 192, 201, 201, 201, 201, 70, 70, 70, 70, 70, 59, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 70, 197, 197, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 70, 70, 70, 70, 70, 29, 29, 1, 70, 70] 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])
total number of confs: 819
number of broken/clashed sets: 70
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497324 none O=C(CCC1CCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 18, 18, 31, 31, 31, 31, 31, 40, 40, 78, 122, 201, 201, 201, 201, 201, 31, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 18, 31, 31, 31, 31, 31, 78, 78, 201, 31, 31] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 35, 36, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 529
number of broken/clashed sets: 70
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497324 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497324
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497324/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497324
Building REAL300025497325
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497325'
/scratch/stefan/7787277/working/building/REAL300025497325 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497325

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497325/0 /scratch/stefan/7787277/working/building/REAL300025497325 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 178)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/178
`/scratch/stefan/7787277/working/3D/178' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2COCCO2)C1)

`REAL300025497325.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497325.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497325/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497325 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2COCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 5, 7, 7, 6, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 16, 36, 122, 121, 122, 122, 122, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 16, 1, 17, 17, 122, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 16, 16, 1, 1] 201
rigid atoms, others: [32, 1, 41, 10, 11, 12, 13, 14, 15, 42, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 248
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497325 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2COCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 5, 7, 7, 6, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [40, 16, 40, 83, 127, 201, 201, 201, 201, 201, 16, 16, 16, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 83, 83, 201, 16, 16, 16, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 16, 16] 201
rigid atoms, others: [34, 35, 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, 41, 42])
total number of confs: 521
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497325 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2COCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 12, 5, 5, 12, 5, 7, 7, 6, 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, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [93, 43, 13, 1, 1, 1, 1, 1, 1, 1, 93, 122, 122, 122, 122, 122, 167, 167, 167, 201, 201, 201, 201, 201, 122, 43, 43, 1, 122, 122, 122, 122, 122, 167, 201, 201, 201, 201, 201, 201, 201, 122, 122] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 650
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497325 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497325
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497325/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497325
Building REAL300025497326
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497326'
/scratch/stefan/7787277/working/building/REAL300025497326 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497326

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497326/0 /scratch/stefan/7787277/working/building/REAL300025497326 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 179)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/179
`/scratch/stefan/7787277/working/3D/179' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NN2)C1)

`REAL300025497326.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497326.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497326/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497326 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 129, 129, 129, 129, 129, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 1, 21, 21, 129, 1, 1, 1, 1, 1, 5, 10, 10, 10, 1, 1] 201
rigid atoms, others: [1, 36, 37, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34, 35])
total number of confs: 249
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497326 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 10, 26, 62, 100, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 62, 62, 201, 10, 10, 10, 10, 10, 4, 1, 1, 1, 10, 10] 201
rigid atoms, others: [33, 34, 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, 36, 37])
total number of confs: 458
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497326 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 42, 13, 1, 1, 1, 1, 1, 1, 1, 96, 129, 129, 129, 129, 129, 188, 188, 188, 201, 201, 201, 201, 129, 42, 42, 1, 129, 129, 129, 129, 129, 188, 201, 201, 201, 129, 129] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 620
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497326 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497326
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497326/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497326
Building REAL300025497327
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497327'
/scratch/stefan/7787277/working/building/REAL300025497327 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497327

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497327/0 /scratch/stefan/7787277/working/building/REAL300025497327 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 180)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/180
`/scratch/stefan/7787277/working/3D/180' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CC=N1)

`REAL300025497327.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497327.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497327/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497327 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 119, 119, 119, 119, 119, 73, 30, 73, 13, 1, 1, 1, 1, 1, 1, 1, 119, 201, 201, 201, 201, 201, 201, 201, 201, 201, 164, 119, 119, 119, 119, 119, 30, 30, 1, 119, 119, 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])
total number of confs: 676
number of broken/clashed sets: 57
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497327 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 11, 11, 11, 25, 25, 25, 25, 25, 43, 43, 80, 118, 201, 201, 201, 201, 201, 25, 1, 1, 1, 1, 1, 6, 6, 6, 6, 11, 25, 25, 25, 25, 25, 80, 80, 201, 25, 25, 1, 1, 1] 201
rigid atoms, others: [1, 41, 42, 43, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 516
number of broken/clashed sets: 57
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497327 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 1, 8, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 29, 119, 119, 119, 119, 119, 1, 15, 25, 25, 25, 25, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 16, 16, 119, 1, 1, 25, 25, 25] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 20, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43])
total number of confs: 264
number of broken/clashed sets: 57
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497327 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497327
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497327/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497327
Building REAL300025497328
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497328'
/scratch/stefan/7787277/working/building/REAL300025497328 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497328

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497328/0 /scratch/stefan/7787277/working/building/REAL300025497328 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 181)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/181
`/scratch/stefan/7787277/working/3D/181' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(CC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497328.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497328.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497328/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497328 none CCCCC(CC)C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 200, 164, 120, 164, 159, 120, 120, 72, 72, 72, 72, 72, 51, 26, 51, 13, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 201, 201, 201, 200, 200, 164, 165, 165, 165, 165, 165, 120, 72, 72, 72, 72, 72, 26, 26, 1, 72, 72] 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])
total number of confs: 848
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497328 none CCCCC(CC)C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [28, 28, 27, 13, 5, 13, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 25, 72, 72, 72, 72, 72, 1, 28, 28, 28, 28, 28, 28, 28, 27, 27, 13, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 13, 13, 72, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49])
total number of confs: 282
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497328 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497328
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497328/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497328
Building REAL300025497329
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497329'
/scratch/stefan/7787277/working/building/REAL300025497329 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497329

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497329/0 /scratch/stefan/7787277/working/building/REAL300025497329 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 182)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/182
`/scratch/stefan/7787277/working/3D/182' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497329.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497329.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497329/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497329 none CSC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
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, 18, 25, 18, 18, 13, 13, 13, 13, 13, 13, 13, 13, 9, 1, 1, 1, 1, 1, 1, 1, 13, 27, 27, 27, 25, 25, 25, 25, 18, 13, 13, 13, 13, 13, 13, 13, 1, 13, 13] 27
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])
total number of confs: 89
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: REAL300025497329 none CSC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 14, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
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: [19, 15, 6, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 13, 13, 13, 13, 13, 1, 19, 19, 19, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 7, 7, 13, 1, 1] 27
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 89
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497329 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497329
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497329/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497329
Building REAL300025497330
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497330'
/scratch/stefan/7787277/working/building/REAL300025497330 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497330

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497330/0 /scratch/stefan/7787277/working/building/REAL300025497330 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 183)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/183
`/scratch/stefan/7787277/working/3D/183' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497330.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497330.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497330/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497330 none CCOC(C)C(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 163, 201, 163, 163, 116, 116, 116, 116, 116, 73, 29, 72, 13, 1, 1, 1, 1, 1, 1, 1, 116, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 116, 116, 116, 116, 116, 29, 29, 1, 116, 116] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43])
total number of confs: 693
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: REAL300025497330 none CCOC(C)C(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 17, 4, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 29, 116, 116, 116, 116, 116, 1, 24, 24, 24, 24, 24, 17, 17, 17, 17, 4, 1, 1, 1, 1, 1, 16, 16, 116, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 264
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497330 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497330
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497330/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497330
Building REAL300025497331
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497331'
/scratch/stefan/7787277/working/building/REAL300025497331 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497331

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497331/0 /scratch/stefan/7787277/working/building/REAL300025497331 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 184)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/184
`/scratch/stefan/7787277/working/3D/184' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)COCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497331.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497331.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497331/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497331 none CC(C)COCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 190, 178, 175, 81, 81, 81, 75, 75, 75, 75, 75, 59, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 75, 201, 201, 201, 201, 201, 201, 201, 201, 201, 178, 178, 175, 175, 81, 75, 75, 75, 75, 75, 29, 29, 1, 75, 75] 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: 753
number of broken/clashed sets: 127
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497331 none CC(C)COCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 37, 45, 22, 14, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 16, 75, 75, 75, 75, 75, 1, 45, 45, 45, 45, 45, 45, 45, 37, 37, 14, 14, 11, 11, 3, 1, 1, 1, 1, 1, 7, 7, 75, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 306
number of broken/clashed sets: 127
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497331 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497331
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497331/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497331
Building REAL300025497332
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497332'
/scratch/stefan/7787277/working/building/REAL300025497332 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497332

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497332/0 /scratch/stefan/7787277/working/building/REAL300025497332 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 185)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/185
`/scratch/stefan/7787277/working/3D/185' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497332.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497332.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497332/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497332 none CCOCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
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, 185, 191, 94, 94, 94, 89, 89, 89, 89, 89, 64, 30, 64, 13, 1, 1, 1, 1, 1, 1, 1, 89, 201, 201, 201, 201, 201, 194, 193, 197, 197, 191, 191, 94, 89, 89, 89, 89, 89, 30, 30, 1, 89, 89] 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])
total number of confs: 795
number of broken/clashed sets: 97
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497332 none CCOCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 18, 13, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 89, 89, 89, 89, 89, 1, 22, 22, 22, 22, 22, 16, 16, 17, 17, 11, 11, 3, 1, 1, 1, 1, 1, 9, 9, 89, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 225
number of broken/clashed sets: 97
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497332 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497332
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497332/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497332
Building REAL300025497333
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497333'
/scratch/stefan/7787277/working/building/REAL300025497333 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497333

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497333/0 /scratch/stefan/7787277/working/building/REAL300025497333 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 186)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/186
`/scratch/stefan/7787277/working/3D/186' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COCC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497333.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497333.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497333/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497333 none O=C(COCC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need 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, 8, 14, 28, 50, 50, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 37, 37, 37, 37, 37, 1, 8, 8, 28, 28, 50, 50, 50, 50, 50, 3, 1, 1, 1, 1, 1, 4, 4, 37, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 227
number of broken/clashed sets: 166
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497333 none O=C(COCC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 111, 124, 147, 201, 201, 37, 37, 37, 37, 37, 37, 28, 37, 13, 1, 1, 1, 1, 1, 1, 1, 37, 111, 111, 147, 147, 201, 201, 201, 201, 201, 42, 37, 37, 37, 37, 37, 28, 28, 1, 37, 37] 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])
total number of confs: 781
number of broken/clashed sets: 166
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497333 none O=C(COCC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 36, 20, 8, 1, 1, 1, 1, 48, 48, 50, 50, 50, 50, 50, 50, 50, 79, 116, 201, 201, 201, 201, 201, 50, 36, 36, 8, 8, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 79, 79, 201, 50, 50] 201
rigid atoms, others: [32, 33, 4, 5, 6, 7, 29, 30, 31] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 520
number of broken/clashed sets: 166
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497333 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497333
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497333/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497333
Building REAL300025497334
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497334'
/scratch/stefan/7787277/working/building/REAL300025497334 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497334

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497334/0 /scratch/stefan/7787277/working/building/REAL300025497334 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 187)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/187
`/scratch/stefan/7787277/working/3D/187' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497334.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497334.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497334/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497334 none O=C(CC1CCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 22, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 27, 86, 86, 86, 86, 86, 1, 22, 22, 30, 30, 30, 30, 30, 30, 30, 4, 1, 1, 1, 1, 1, 12, 12, 86, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 248
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497334 none O=C(CC1CCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [118, 118, 118, 197, 201, 201, 201, 201, 86, 86, 86, 86, 86, 60, 29, 60, 13, 1, 1, 1, 1, 1, 1, 1, 86, 197, 197, 201, 201, 201, 201, 201, 201, 201, 118, 86, 86, 86, 86, 86, 29, 29, 1, 86, 86] 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])
total number of confs: 725
number of broken/clashed sets: 60
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497334 none O=C(CC1CCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 16, 16, 30, 30, 30, 30, 30, 44, 44, 78, 122, 201, 201, 201, 201, 201, 30, 6, 6, 1, 1, 1, 1, 1, 1, 1, 16, 30, 30, 30, 30, 30, 78, 78, 201, 30, 30] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 27, 28, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 534
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497334 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497334
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497334/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497334
Building REAL300025497335
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497335'
/scratch/stefan/7787277/working/building/REAL300025497335 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497335

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497335/0 /scratch/stefan/7787277/working/building/REAL300025497335 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 188)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/188
`/scratch/stefan/7787277/working/3D/188' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=N1)

`REAL300025497335.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497335.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497335/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497335 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 8, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 24, 84, 84, 84, 84, 84, 1, 18, 18, 18, 18, 18, 18, 4, 1, 1, 1, 1, 1, 11, 11, 84, 1, 1, 18] 201
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 37, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39])
total number of confs: 164
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497335 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 8, 7, 7, 7, 6, 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]
0  hydrogens need rotated
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, 84, 84, 84, 84, 84, 71, 44, 71, 13, 1, 1, 1, 1, 1, 1, 1, 84, 201, 201, 201, 201, 201, 201, 129, 84, 84, 84, 84, 84, 44, 44, 1, 84, 84, 201] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39])
total number of confs: 555
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497335 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 8, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 18, 18, 18, 18, 18, 36, 36, 63, 104, 201, 201, 201, 201, 201, 18, 1, 1, 1, 2, 2, 2, 8, 18, 18, 18, 18, 18, 63, 63, 201, 18, 18, 1] 201
rigid atoms, others: [0, 1, 2, 3, 39, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 466
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497335 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497335
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497335/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497335
Building REAL300025497336
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497336'
/scratch/stefan/7787277/working/building/REAL300025497336 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497336

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497336/0 /scratch/stefan/7787277/working/building/REAL300025497336 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 189)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/189
`/scratch/stefan/7787277/working/3D/189' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CNN=C2)C1)

`REAL300025497336.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497336.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497336/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497336 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CNN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 20, 49, 161, 161, 161, 161, 161, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 1, 20, 20, 161, 1, 1, 1, 1, 1, 5, 8, 8, 8, 1, 1] 201
rigid atoms, others: [1, 36, 37, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34, 35])
total number of confs: 289
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497336 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CNN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 10, 31, 68, 119, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 10, 68, 68, 201, 10, 10, 10, 10, 10, 4, 1, 1, 1, 10, 10] 201
rigid atoms, others: [33, 34, 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, 36, 37])
total number of confs: 474
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497336 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CNN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 8, 1, 5, 7, 7, 6, 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, 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: [121, 53, 13, 1, 1, 1, 1, 1, 1, 1, 121, 161, 161, 161, 161, 161, 201, 201, 201, 201, 201, 201, 201, 161, 53, 53, 1, 161, 161, 161, 161, 161, 201, 201, 201, 201, 161, 161] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 599
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497336 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497336
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497336/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497336
Building REAL300025497337
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497337'
/scratch/stefan/7787277/working/building/REAL300025497337 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497337

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497337/0 /scratch/stefan/7787277/working/building/REAL300025497337 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 190)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/190
`/scratch/stefan/7787277/working/3D/190' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CNC(=O)C1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497337.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497337.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497337/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497337 none O=C(CNC(=O)C1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 5, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 12, 13, 13, 13, 33, 33, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 14, 66, 66, 66, 66, 66, 1, 12, 12, 13, 33, 33, 33, 33, 33, 2, 1, 1, 1, 1, 1, 7, 7, 66, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 206
number of broken/clashed sets: 111
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497337 none O=C(CNC(=O)C1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 5, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 129, 131, 131, 131, 201, 201, 66, 66, 66, 66, 66, 48, 30, 48, 13, 1, 1, 1, 1, 1, 1, 1, 66, 129, 129, 131, 201, 201, 201, 201, 201, 66, 66, 66, 66, 66, 66, 30, 30, 1, 66, 66] 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])
total number of confs: 770
number of broken/clashed sets: 111
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497337 none O=C(CNC(=O)C1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 5, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 15, 7, 7, 1, 7, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 40, 40, 66, 115, 201, 201, 201, 201, 201, 33, 15, 15, 7, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 66, 66, 201, 33, 33] 201
rigid atoms, others: [32, 33, 4, 6, 7, 8, 29, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 472
number of broken/clashed sets: 111
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497337 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497337
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497337/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497337
Building REAL300025497338
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497338'
/scratch/stefan/7787277/working/building/REAL300025497338 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497338

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497338/0 /scratch/stefan/7787277/working/building/REAL300025497338 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 191)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/191
`/scratch/stefan/7787277/working/3D/191' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497338.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497338.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497338/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497338 none COCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
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, 194, 94, 94, 94, 86, 86, 86, 86, 86, 63, 29, 63, 13, 1, 1, 1, 1, 1, 1, 1, 86, 201, 201, 201, 193, 195, 199, 199, 194, 194, 94, 86, 86, 86, 86, 86, 29, 29, 1, 86, 86] 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])
total number of confs: 814
number of broken/clashed sets: 98
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497338 none COCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 22, 15, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 18, 86, 86, 86, 86, 86, 1, 26, 26, 26, 20, 20, 19, 19, 12, 12, 4, 1, 1, 1, 1, 1, 9, 9, 86, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 242
number of broken/clashed sets: 98
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497338 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497338
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497338/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497338
Building REAL300025497339
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497339'
/scratch/stefan/7787277/working/building/REAL300025497339 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497339

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497339/0 /scratch/stefan/7787277/working/building/REAL300025497339 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 192)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/192
`/scratch/stefan/7787277/working/3D/192' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497339.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497339.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497339/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497339 none O=C(COC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 14, 67, 67, 67, 67, 67, 1, 10, 10, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 1, 1, 1, 1, 1, 7, 7, 67, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 195
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497339 none O=C(COC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 159, 173, 201, 201, 201, 201, 67, 67, 67, 67, 67, 54, 31, 54, 13, 1, 1, 1, 1, 1, 1, 1, 67, 159, 159, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 67, 67, 67, 67, 67, 31, 31, 1, 67, 67] 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])
total number of confs: 770
number of broken/clashed sets: 83
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497339 none O=C(COC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 15, 5, 1, 1, 1, 1, 1, 1, 28, 28, 35, 35, 35, 35, 35, 44, 44, 86, 133, 201, 201, 201, 201, 201, 35, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 35, 35, 35, 35, 35, 86, 86, 201, 35, 35] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 35, 36, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 539
number of broken/clashed sets: 83
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497339 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497339
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497339/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497339
Building REAL300025497340
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497340'
/scratch/stefan/7787277/working/building/REAL300025497340 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497340

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497340/0 /scratch/stefan/7787277/working/building/REAL300025497340 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 193)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/193
`/scratch/stefan/7787277/working/3D/193' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497340.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497340.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497340/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497340 none CC1=NC=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 25, 25, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 31, 69, 69, 69, 69, 69, 1, 25, 25, 25, 5, 25, 5, 1, 1, 1, 1, 1, 18, 18, 69, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 209
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497340 none CC1=NC=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 95, 201, 201, 95, 95, 95, 69, 69, 69, 69, 69, 58, 38, 58, 13, 1, 1, 1, 1, 1, 1, 1, 69, 201, 201, 201, 102, 201, 95, 69, 69, 69, 69, 69, 38, 38, 1, 69, 69] 201
rigid atoms, others: [39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41])
total number of confs: 730
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497340 none CC1=NC=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 25, 25, 25, 25, 25, 50, 50, 88, 132, 201, 201, 201, 201, 201, 25, 2, 2, 2, 1, 1, 9, 25, 25, 25, 25, 25, 88, 88, 201, 25, 25] 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])
total number of confs: 543
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497340 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497340
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497340/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497340
Building REAL300025497341
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497341'
/scratch/stefan/7787277/working/building/REAL300025497341 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497341

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497341/0 /scratch/stefan/7787277/working/building/REAL300025497341 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 194)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/194
`/scratch/stefan/7787277/working/3D/194' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCSCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497341.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497341.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497341/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497341 none CCSCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 14, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 184, 179, 81, 81, 81, 81, 81, 81, 81, 81, 60, 29, 60, 13, 1, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 201, 201, 184, 184, 179, 179, 81, 81, 81, 81, 81, 81, 29, 29, 1, 81, 81] 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])
total number of confs: 731
number of broken/clashed sets: 114
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497341 none CCSCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 14, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [45, 38, 11, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 15, 81, 81, 81, 81, 81, 1, 45, 45, 45, 45, 45, 11, 11, 9, 9, 2, 1, 1, 1, 1, 1, 7, 7, 81, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 236
number of broken/clashed sets: 114
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497341 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497341
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497341/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497341
Building REAL300025497342
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497342'
/scratch/stefan/7787277/working/building/REAL300025497342 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497342

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497342/0 /scratch/stefan/7787277/working/building/REAL300025497342 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 195)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/195
`/scratch/stefan/7787277/working/3D/195' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497342.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497342.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497342/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497342 none CCOC1CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 23, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 27, 100, 100, 100, 100, 100, 1, 25, 25, 25, 25, 25, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 12, 12, 100, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 223
number of broken/clashed sets: 65
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497342 none CCOC1CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 137, 137, 137, 100, 100, 100, 100, 100, 77, 31, 77, 13, 1, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 100, 100, 100, 100, 100, 31, 31, 1, 100, 100] 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])
total number of confs: 653
number of broken/clashed sets: 65
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497342 none CCOC1CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 4, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 28, 28, 64, 106, 201, 201, 201, 201, 201, 14, 5, 5, 5, 5, 5, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 64, 64, 201, 14, 14] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 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, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 481
number of broken/clashed sets: 65
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497342 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497342
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497342/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497342
Building REAL300025497343
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497343'
/scratch/stefan/7787277/working/building/REAL300025497343 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497343

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497343/0 /scratch/stefan/7787277/working/building/REAL300025497343 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 196)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/196
`/scratch/stefan/7787277/working/3D/196' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NSN=C2)C1)

`REAL300025497343.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497343.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497343/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497343 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NSN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 14, 8, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 23, 50, 139, 139, 139, 139, 139, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 1, 23, 23, 139, 1, 1, 1, 1, 1, 6, 10, 1, 1] 201
rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 33, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26])
total number of confs: 270
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497343 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NSN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 14, 8, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 25, 59, 101, 201, 201, 201, 201, 201, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 10, 59, 59, 201, 10, 10, 10, 10, 10, 3, 1, 10, 10] 201
rigid atoms, others: [33, 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, 34, 35])
total number of confs: 440
number of broken/clashed sets: 39
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497343 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NSN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 14, 8, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 52, 13, 1, 1, 1, 1, 1, 1, 1, 109, 139, 139, 139, 139, 139, 201, 201, 201, 201, 201, 201, 201, 139, 52, 52, 1, 139, 139, 139, 139, 139, 201, 201, 139, 139] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 639
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497343 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497343
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497343/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497343
Building REAL300025497344
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497344'
/scratch/stefan/7787277/working/building/REAL300025497344 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497344

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497344/0 /scratch/stefan/7787277/working/building/REAL300025497344 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 197)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/197
`/scratch/stefan/7787277/working/3D/197' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=NS2)C1)

`REAL300025497344.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497344.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497344/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497344 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=NS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 8, 14, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 108, 108, 108, 108, 108, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 1, 16, 16, 108, 1, 1, 1, 1, 1, 4, 12, 1, 1] 201
rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 33, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26])
total number of confs: 206
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497344 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=NS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 8, 14, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 12, 29, 63, 103, 201, 201, 201, 201, 201, 12, 12, 12, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 12, 63, 63, 201, 12, 12, 12, 12, 12, 5, 1, 12, 12] 201
rigid atoms, others: [33, 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, 34, 35])
total number of confs: 461
number of broken/clashed sets: 29
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497344 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=NS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 8, 14, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 108, 108, 108, 108, 108, 153, 153, 153, 201, 201, 201, 201, 108, 46, 46, 1, 108, 108, 108, 108, 108, 153, 201, 108, 108] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 579
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497344 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497344
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497344/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497344
Building REAL300025497345
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497345'
/scratch/stefan/7787277/working/building/REAL300025497345 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497345

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497345/0 /scratch/stefan/7787277/working/building/REAL300025497345 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 198)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/198
`/scratch/stefan/7787277/working/3D/198' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497345.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497345.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497345/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497345 none COC(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
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, 201, 168, 72, 72, 72, 46, 46, 46, 46, 46, 39, 26, 39, 12, 1, 1, 1, 1, 1, 1, 1, 46, 201, 201, 201, 180, 168, 168, 72, 46, 46, 46, 46, 46, 26, 26, 1, 46, 46] 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])
total number of confs: 764
number of broken/clashed sets: 57
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497345 none COC(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 31, 35, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 11, 46, 46, 46, 46, 46, 1, 35, 35, 35, 31, 23, 23, 5, 1, 1, 1, 1, 1, 6, 6, 46, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 192
number of broken/clashed sets: 57
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497345 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497345
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497345/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497345
Building REAL300025497346
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497346'
/scratch/stefan/7787277/working/building/REAL300025497346 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497346

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497346/0 /scratch/stefan/7787277/working/building/REAL300025497346 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 199)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/199
`/scratch/stefan/7787277/working/3D/199' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NOC=C2)C1)

`REAL300025497346.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497346.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497346/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497346 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NOC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 22, 51, 146, 146, 146, 146, 146, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 1, 22, 22, 146, 1, 1, 1, 1, 1, 6, 11, 11, 1, 1] 201
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34])
total number of confs: 279
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497346 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NOC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 11, 31, 62, 109, 201, 201, 201, 201, 201, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 11, 62, 62, 201, 11, 11, 11, 11, 11, 3, 1, 1, 11, 11] 201
rigid atoms, others: [33, 34, 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, 35, 36])
total number of confs: 444
number of broken/clashed sets: 43
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497346 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NOC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [111, 48, 13, 1, 1, 1, 1, 1, 1, 1, 111, 146, 146, 146, 146, 146, 201, 201, 201, 201, 201, 201, 201, 146, 48, 48, 1, 146, 146, 146, 146, 146, 201, 201, 201, 146, 146] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 621
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497346 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497346
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497346/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497346
Building REAL300025497347
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497347'
/scratch/stefan/7787277/working/building/REAL300025497347 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497347

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497347/0 /scratch/stefan/7787277/working/building/REAL300025497347 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 200)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/200
`/scratch/stefan/7787277/working/3D/200' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCSCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497347.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497347.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497347/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497347 none CCCSCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 166, 151, 82, 82, 82, 82, 82, 82, 82, 82, 62, 31, 62, 13, 1, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 201, 201, 201, 201, 151, 151, 82, 82, 82, 82, 82, 82, 31, 31, 1, 82, 82] 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])
total number of confs: 772
number of broken/clashed sets: 139
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497347 none CCCSCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [38, 38, 19, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 19, 82, 82, 82, 82, 82, 1, 38, 38, 38, 38, 38, 38, 38, 8, 8, 2, 1, 1, 1, 1, 1, 8, 8, 82, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 263
number of broken/clashed sets: 139
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497347 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497347
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497347/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497347
Building REAL300025497348
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497348'
/scratch/stefan/7787277/working/building/REAL300025497348 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497348

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497348/0 /scratch/stefan/7787277/working/building/REAL300025497348 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 201)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/201
`/scratch/stefan/7787277/working/3D/201' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1)

`REAL300025497348.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497348.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497348/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497348 none CC(=CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 1, 11, 8, 5, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [122, 122, 83, 83, 83, 50, 50, 50, 50, 50, 44, 26, 44, 13, 1, 1, 1, 1, 1, 1, 1, 50, 122, 201, 201, 122, 122, 122, 122, 83, 50, 50, 50, 50, 50, 26, 26, 1, 50, 50, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 721
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497348 none CC(=CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 1, 11, 8, 5, 1, 1, 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, 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]
0  hydrogens need 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, 17, 17, 17, 37, 37, 37, 37, 37, 54, 54, 98, 144, 201, 201, 201, 201, 201, 37, 1, 1, 1, 3, 3, 3, 3, 17, 37, 37, 37, 37, 37, 98, 98, 201, 37, 37, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 40, 41, 42, 43, 44, 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])
total number of confs: 560
number of broken/clashed sets: 66
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497348 none CC(=CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 1, 11, 8, 5, 1, 1, 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, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 50, 50, 50, 50, 50, 1, 20, 37, 37, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 6, 6, 50, 1, 1, 37, 37, 37, 37, 37] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 21, 39, 38, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44])
total number of confs: 191
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497348 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497348
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497348/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497348
Building REAL300025497349
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497349'
/scratch/stefan/7787277/working/building/REAL300025497349 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497349

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497349/0 /scratch/stefan/7787277/working/building/REAL300025497349 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 202)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/202
`/scratch/stefan/7787277/working/3D/202' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497349.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497349.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497349/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497349 none CC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 6, 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]
0  hydrogens 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, 33, 58, 157, 157, 157, 157, 157, 1, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 33, 33, 157, 1, 1, 13] 201
rigid atoms, others: [32, 33, 34, 38, 7, 8, 9, 10, 11, 12, 13, 23, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40])
total number of confs: 320
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497349 none CC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 6, 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]
0  hydrogens need rotated
201  conformations 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, 157, 157, 157, 157, 157, 110, 45, 110, 13, 1, 1, 1, 1, 1, 1, 1, 156, 201, 201, 201, 201, 201, 197, 157, 157, 157, 157, 157, 45, 45, 1, 157, 157, 201] 201
rigid atoms, others: [37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 602
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497349 none CC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 39, 39, 100, 131, 201, 201, 201, 201, 201, 13, 1, 2, 2, 2, 1, 4, 13, 13, 13, 13, 13, 100, 100, 201, 13, 13, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 24, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 560
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497349 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497349
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497349/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497349
Building REAL300025497350
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497350'
/scratch/stefan/7787277/working/building/REAL300025497350 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497350

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497350/0 /scratch/stefan/7787277/working/building/REAL300025497350 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 203)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/203
`/scratch/stefan/7787277/working/3D/203' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CS2)C1)

`REAL300025497350.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497350.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497350/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497350 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 18, 43, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 1, 18, 18, 130, 1, 1, 1, 1, 1, 4, 14, 14, 1, 1] 201
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34])
total number of confs: 244
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497350 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 32, 69, 113, 201, 201, 201, 201, 201, 14, 14, 14, 14, 8, 8, 1, 8, 1, 1, 1, 1, 1, 14, 69, 69, 201, 14, 14, 14, 14, 14, 8, 1, 1, 14, 14] 201
rigid atoms, others: [33, 34, 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, 35, 36])
total number of confs: 475
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497350 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 14, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 50, 13, 1, 1, 1, 1, 1, 1, 1, 102, 130, 130, 130, 130, 130, 188, 188, 188, 201, 201, 201, 201, 130, 50, 50, 1, 130, 130, 130, 130, 130, 188, 201, 201, 130, 130] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 606
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497350 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497350
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497350/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497350
Building REAL300025497351
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497351'
/scratch/stefan/7787277/working/building/REAL300025497351 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497351

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497351/0 /scratch/stefan/7787277/working/building/REAL300025497351 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 204)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/204
`/scratch/stefan/7787277/working/3D/204' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497351.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497351.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497351/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497351 none CC1=NN(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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: [16, 16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 37, 100, 100, 100, 100, 100, 1, 16, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 22, 22, 100, 1, 1, 16] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 224
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497351 none CC1=NN(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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, 135, 135, 135, 100, 100, 100, 100, 100, 77, 38, 77, 13, 1, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 201, 201, 201, 135, 100, 100, 100, 100, 100, 38, 38, 1, 100, 100, 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])
total number of confs: 568
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497351 none CC1=NN(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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, 6, 6, 6, 16, 16, 16, 16, 16, 41, 41, 85, 121, 201, 201, 201, 201, 201, 16, 1, 2, 2, 2, 2, 2, 2, 6, 16, 16, 16, 16, 16, 85, 85, 201, 16, 16, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 43, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 542
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497351 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497351
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497351/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497351
Building REAL300025497352
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497352'
/scratch/stefan/7787277/working/building/REAL300025497352 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497352

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497352/0 /scratch/stefan/7787277/working/building/REAL300025497352 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 205)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/205
`/scratch/stefan/7787277/working/3D/205' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1)

`REAL300025497352.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497352.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497352/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497352 none CC1=CN(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.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, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 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: [25, 25, 25, 19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 87, 87, 87, 87, 87, 1, 25, 25, 25, 25, 25, 25, 19, 19, 5, 1, 1, 1, 1, 1, 13, 13, 87, 1, 1, 25] 201
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 221
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497352 none CC1=CN(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.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, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 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, 116, 116, 116, 87, 87, 87, 87, 87, 53, 29, 53, 13, 1, 1, 1, 1, 1, 1, 1, 87, 201, 201, 201, 201, 201, 201, 201, 201, 116, 87, 87, 87, 87, 87, 29, 29, 1, 87, 87, 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])
total number of confs: 803
number of broken/clashed sets: 53
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497352 none CC1=CN(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.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, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 6, 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, 7, 15, 15, 15, 25, 25, 25, 25, 25, 42, 42, 73, 115, 201, 201, 201, 201, 201, 25, 1, 1, 2, 2, 2, 1, 7, 7, 15, 25, 25, 25, 25, 25, 73, 73, 201, 25, 25, 1] 201
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: 518
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497352 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497352
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497352/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497352
Building REAL300025497353
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497353'
/scratch/stefan/7787277/working/building/REAL300025497353 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497353

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497353/0 /scratch/stefan/7787277/working/building/REAL300025497353 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 206)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/206
`/scratch/stefan/7787277/working/3D/206' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)COC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497353.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497353.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497353/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497353 none CC(C)COC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 188, 175, 124, 175, 124, 124, 62, 62, 62, 62, 62, 52, 29, 51, 13, 1, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 175, 175, 124, 62, 62, 62, 62, 62, 29, 29, 1, 62, 62] 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: 776
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: REAL300025497353 none CC(C)COC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 25, 38, 12, 8, 4, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 14, 62, 62, 62, 62, 62, 1, 38, 38, 38, 38, 38, 38, 38, 25, 25, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 8, 8, 62, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 277
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497353 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497353
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497353/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497353
Building REAL300025497354
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497354'
/scratch/stefan/7787277/working/building/REAL300025497354 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497354

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497354/0 /scratch/stefan/7787277/working/building/REAL300025497354 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 207)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/207
`/scratch/stefan/7787277/working/3D/207' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497354.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497354.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497354/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497354 none CCCC(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 139, 139, 139, 139, 60, 60, 60, 60, 60, 60, 60, 60, 45, 28, 45, 13, 1, 1, 1, 1, 1, 1, 1, 60, 201, 201, 201, 201, 201, 201, 201, 139, 139, 139, 60, 60, 60, 60, 60, 60, 28, 28, 1, 60, 60] 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])
total number of confs: 891
number of broken/clashed sets: 148
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497354 none CCCC(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 10, 10, 10, 10, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 14, 60, 60, 60, 60, 60, 1, 47, 47, 47, 47, 47, 41, 41, 10, 10, 10, 2, 1, 1, 1, 1, 1, 7, 7, 60, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 318
number of broken/clashed sets: 148
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497354 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497354
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497354/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497354
Building REAL300025497355
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497355'
/scratch/stefan/7787277/working/building/REAL300025497355 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497355

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497355/0 /scratch/stefan/7787277/working/building/REAL300025497355 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 208)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/208
`/scratch/stefan/7787277/working/3D/208' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC=C(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497355.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497355.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497355/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497355 none CCC=C(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 1, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 197, 197, 95, 197, 95, 95, 77, 77, 77, 77, 77, 53, 28, 53, 13, 1, 1, 1, 1, 1, 1, 1, 77, 201, 201, 201, 201, 201, 197, 197, 197, 197, 95, 77, 77, 77, 77, 77, 28, 28, 1, 77, 77] 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])
total number of confs: 604
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: REAL300025497355 none CCC=C(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 1, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [33, 18, 18, 5, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 25, 77, 77, 77, 77, 77, 1, 33, 33, 33, 33, 33, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 12, 12, 77, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 252
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497355 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497355
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497355/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497355
Building REAL300025497356
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497356'
/scratch/stefan/7787277/working/building/REAL300025497356 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497356

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497356/0 /scratch/stefan/7787277/working/building/REAL300025497356 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 209)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/209
`/scratch/stefan/7787277/working/3D/209' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497356.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497356.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497356/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497356 none CS(=O)(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 14, 11, 11, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 128, 128, 128, 83, 83, 83, 83, 83, 75, 53, 75, 13, 1, 1, 1, 1, 1, 1, 1, 83, 201, 201, 201, 200, 200, 128, 83, 83, 83, 83, 83, 53, 53, 1, 83, 83] 201
rigid atoms, others: [37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 828
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: REAL300025497356 none CS(=O)(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 14, 11, 11, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 35, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 17, 83, 83, 83, 83, 83, 1, 35, 35, 35, 20, 20, 5, 1, 1, 1, 1, 1, 12, 12, 83, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 7, 8, 9, 10, 11, 12, 13, 23, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 277
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497356 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497356
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497356/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497356
Building REAL300025497357
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497357'
/scratch/stefan/7787277/working/building/REAL300025497357 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497357

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497357/0 /scratch/stefan/7787277/working/building/REAL300025497357 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 210)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/210
`/scratch/stefan/7787277/working/3D/210' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=C1CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497357.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497357.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497357/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497357 none O=C(C=C1CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 34, 111, 111, 111, 111, 111, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 19, 19, 111, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 239
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497357 none O=C(C=C1CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 111, 111, 111, 111, 111, 83, 41, 83, 13, 1, 1, 1, 1, 1, 1, 1, 111, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 111, 111, 111, 111, 111, 41, 41, 1, 111, 111] 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])
total number of confs: 677
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497357 none O=C(C=C1CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 14, 14, 14, 14, 50, 50, 96, 131, 201, 201, 201, 201, 201, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 14, 96, 96, 201, 14, 14] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33, 35, 36, 26, 27, 28, 29, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 545
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497357 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497357
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497357/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497357
Building REAL300025497358
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497358'
/scratch/stefan/7787277/working/building/REAL300025497358 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497358

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497358/0 /scratch/stefan/7787277/working/building/REAL300025497358 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 211)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/211
`/scratch/stefan/7787277/working/3D/211' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=CO1)

`REAL300025497358.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497358.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497358/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497358 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 12, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 39, 138, 138, 138, 138, 138, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 16, 16, 138, 1, 1, 11] 201
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 37, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39])
total number of confs: 242
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497358 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 12, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 191, 191, 191, 138, 138, 138, 138, 138, 110, 44, 110, 13, 1, 1, 1, 1, 1, 1, 1, 138, 201, 201, 201, 201, 201, 201, 191, 138, 138, 138, 138, 138, 44, 44, 1, 138, 138, 201] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39])
total number of confs: 599
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497358 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 12, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 33, 33, 74, 122, 201, 201, 201, 201, 201, 11, 1, 1, 1, 2, 2, 2, 4, 11, 11, 11, 11, 11, 74, 74, 201, 11, 11, 1] 201
rigid atoms, others: [0, 1, 2, 3, 39, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 501
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497358 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497358
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497358/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497358
Building REAL300025497359
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497359'
/scratch/stefan/7787277/working/building/REAL300025497359 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497359

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497359/0 /scratch/stefan/7787277/working/building/REAL300025497359 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 212)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/212
`/scratch/stefan/7787277/working/3D/212' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(CC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497359.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497359.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497359/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497359 none CCOC(CC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 147, 201, 190, 147, 147, 115, 115, 115, 115, 115, 69, 31, 69, 13, 1, 1, 1, 1, 1, 1, 1, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 115, 115, 115, 115, 115, 31, 31, 1, 115, 115] 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])
total number of confs: 779
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: REAL300025497359 none CCOC(CC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 5, 11, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 26, 115, 115, 115, 115, 115, 1, 11, 11, 11, 11, 11, 11, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 13, 13, 115, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 279
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497359 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497359
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497359/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497359
Building REAL300025497360
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497360'
/scratch/stefan/7787277/working/building/REAL300025497360 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497360

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497360/0 /scratch/stefan/7787277/working/building/REAL300025497360 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 213)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/213
`/scratch/stefan/7787277/working/3D/213' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC(F)(F)F)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497360.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497360.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497360/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497360 none O=C(CC(F)(F)F)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 15, 15, 15, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [118, 118, 118, 201, 201, 201, 201, 90, 90, 90, 90, 90, 80, 43, 80, 13, 1, 1, 1, 1, 1, 1, 1, 90, 201, 201, 118, 90, 90, 90, 90, 90, 43, 43, 1, 90, 90] 201
rigid atoms, others: [34, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36])
total number of confs: 776
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: REAL300025497360 none O=C(CC(F)(F)F)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 15, 15, 15, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 24, 90, 90, 90, 90, 90, 1, 26, 26, 5, 1, 1, 1, 1, 1, 13, 13, 90, 1, 1] 201
rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 13, 23, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34])
total number of confs: 229
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497360 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497360
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497360/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497360
Building REAL300025497361
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497361'
/scratch/stefan/7787277/working/building/REAL300025497361 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497361

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497361/0 /scratch/stefan/7787277/working/building/REAL300025497361 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 214)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/214
`/scratch/stefan/7787277/working/3D/214' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497361.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497361.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497361/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497361 none COC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 16, 18, 16, 16, 13, 13, 13, 13, 13, 13, 13, 13, 9, 1, 1, 1, 1, 1, 1, 1, 13, 18, 18, 18, 18, 18, 18, 18, 16, 13, 13, 13, 13, 13, 13, 13, 1, 13, 13] 18
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])
total number of confs: 56
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: REAL300025497361 none COC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [13, 12, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 13, 13, 13, 13, 13, 1, 13, 13, 13, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 7, 7, 13, 1, 1] 18
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 75
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497361 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497361
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497361/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497361
Building REAL300025497362
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497362'
/scratch/stefan/7787277/working/building/REAL300025497362 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497362

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497362/0 /scratch/stefan/7787277/working/building/REAL300025497362 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 215)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/215
`/scratch/stefan/7787277/working/3D/215' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497362.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497362.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497362/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497362 none CC(C)OCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 190, 201, 169, 108, 108, 108, 69, 69, 69, 69, 69, 52, 30, 52, 13, 1, 1, 1, 1, 1, 1, 1, 69, 201, 201, 201, 201, 201, 201, 201, 169, 169, 108, 69, 69, 69, 69, 69, 30, 30, 1, 69, 69] 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])
total number of confs: 755
number of broken/clashed sets: 85
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497362 none CC(C)OCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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
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, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 15, 69, 69, 69, 69, 69, 1, 37, 37, 37, 37, 37, 37, 37, 11, 11, 5, 1, 1, 1, 1, 1, 8, 8, 69, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 223
number of broken/clashed sets: 85
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497362 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497362
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497362/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497362
Building REAL300025497363
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497363'
/scratch/stefan/7787277/working/building/REAL300025497363 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497363

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497363/0 /scratch/stefan/7787277/working/building/REAL300025497363 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 216)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/216
`/scratch/stefan/7787277/working/3D/216' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(OCC1CC1)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497363.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497363.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497363/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497363 none CC(OCC1CC1)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 3, 6, 8, 15, 33, 33, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 18, 65, 65, 65, 65, 65, 1, 6, 6, 6, 6, 15, 15, 33, 33, 33, 33, 33, 3, 1, 1, 1, 1, 1, 8, 8, 65, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 216
number of broken/clashed sets: 121
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497363 none CC(OCC1CC1)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 69, 106, 110, 135, 201, 201, 69, 69, 65, 65, 65, 65, 65, 54, 27, 54, 13, 1, 1, 1, 1, 1, 1, 1, 65, 106, 106, 106, 106, 135, 135, 201, 201, 201, 201, 201, 69, 65, 65, 65, 65, 65, 27, 27, 1, 65, 65] 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])
total number of confs: 811
number of broken/clashed sets: 121
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497363 none CC(OCC1CC1)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 15, 6, 1, 1, 1, 1, 22, 32, 32, 32, 33, 33, 33, 33, 33, 37, 37, 70, 115, 201, 201, 201, 201, 201, 33, 22, 22, 22, 22, 6, 6, 1, 1, 1, 1, 1, 32, 33, 33, 33, 33, 33, 70, 70, 201, 33, 33] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 35, 36] 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 505
number of broken/clashed sets: 121
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497363 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497363
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497363/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497363
Building REAL300025497364
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497364'
/scratch/stefan/7787277/working/building/REAL300025497364 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497364

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497364/0 /scratch/stefan/7787277/working/building/REAL300025497364 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 217)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/217
`/scratch/stefan/7787277/working/3D/217' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497364.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497364.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497364/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497364 none CCCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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
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, 171, 95, 95, 95, 94, 94, 94, 94, 94, 68, 30, 68, 13, 1, 1, 1, 1, 1, 1, 1, 94, 201, 201, 201, 201, 201, 201, 201, 171, 171, 95, 94, 94, 94, 94, 94, 30, 30, 1, 94, 94] 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])
total number of confs: 686
number of broken/clashed sets: 129
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497364 none CCCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 23, 12, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 18, 94, 94, 94, 94, 94, 1, 36, 36, 36, 36, 36, 23, 23, 7, 7, 3, 1, 1, 1, 1, 1, 8, 8, 94, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 287
number of broken/clashed sets: 129
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497364 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497364
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497364/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497364
Building REAL300025497365
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497365'
/scratch/stefan/7787277/working/building/REAL300025497365 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497365

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497365/0 /scratch/stefan/7787277/working/building/REAL300025497365 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 218)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/218
`/scratch/stefan/7787277/working/3D/218' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCOC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497365.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497365.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497365/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497365 none CCCCOC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
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, 117, 106, 73, 106, 73, 73, 43, 43, 43, 43, 43, 38, 27, 37, 13, 1, 1, 1, 1, 1, 1, 1, 43, 201, 201, 201, 201, 201, 201, 201, 128, 128, 106, 106, 106, 106, 73, 43, 43, 43, 43, 43, 27, 27, 1, 43, 43] 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: 870
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497365 none CCCCOC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 45, 22, 10, 8, 4, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 12, 43, 43, 43, 43, 43, 1, 45, 45, 45, 45, 45, 45, 45, 22, 22, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 7, 7, 43, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 278
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497365 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497365
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497365/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497365
Building REAL300025497366
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497366'
/scratch/stefan/7787277/working/building/REAL300025497366 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497366

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497366/0 /scratch/stefan/7787277/working/building/REAL300025497366 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 219)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/219
`/scratch/stefan/7787277/working/3D/219' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCOC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497366.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497366.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497366/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497366 none C=CCCOC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
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, 128, 122, 92, 122, 92, 92, 61, 61, 61, 61, 61, 51, 26, 50, 12, 1, 1, 1, 1, 1, 1, 1, 61, 201, 201, 201, 201, 201, 145, 145, 122, 122, 122, 122, 92, 61, 61, 61, 61, 61, 26, 26, 1, 61, 61] 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])
total number of confs: 880
number of broken/clashed sets: 75
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497366 none C=CCCOC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 11, 7, 6, 4, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 15, 61, 61, 61, 61, 61, 1, 27, 27, 27, 22, 22, 11, 11, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 8, 8, 61, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 205
number of broken/clashed sets: 75
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497366 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497366
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497366/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497366
Building REAL300025497367
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497367'
/scratch/stefan/7787277/working/building/REAL300025497367 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497367

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497367/0 /scratch/stefan/7787277/working/building/REAL300025497367 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 220)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/220
`/scratch/stefan/7787277/working/3D/220' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCOC2)C1)

`REAL300025497367.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497367.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497367/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497367 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCOC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 33, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 1, 17, 17, 95, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 16, 16, 1, 1] 201
rigid atoms, others: [1, 40, 41, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 215
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497367 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCOC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 16, 36, 72, 108, 201, 201, 201, 201, 201, 16, 16, 16, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 16, 72, 72, 201, 16, 16, 16, 16, 16, 8, 1, 1, 1, 1, 1, 1, 1, 16, 16] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 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, 40, 41])
total number of confs: 492
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497367 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCOC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 12, 5, 5, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 13, 1, 1, 1, 1, 1, 1, 1, 69, 95, 95, 95, 95, 95, 141, 141, 141, 201, 201, 201, 201, 95, 38, 38, 1, 95, 95, 95, 95, 95, 141, 201, 201, 201, 201, 201, 201, 201, 95, 95] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 619
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497367 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497367
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497367/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497367
Building REAL300025497368
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497368'
/scratch/stefan/7787277/working/building/REAL300025497368 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497368

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497368/0 /scratch/stefan/7787277/working/building/REAL300025497368 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 221)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/221
`/scratch/stefan/7787277/working/3D/221' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NC(F)=C2)C1)

`REAL300025497368.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497368.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497368/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497368 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NC(F)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 5, 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, 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, 13, 21, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 14, 1, 13, 13, 60, 1, 1, 1, 1, 1, 5, 14, 14, 14, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37])
total number of confs: 140
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497368 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NC(F)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 5, 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, 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: [36, 14, 36, 76, 110, 201, 201, 201, 201, 201, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 76, 76, 201, 14, 14, 14, 14, 14, 5, 1, 1, 1, 14, 14] 201
rigid atoms, others: [35, 36, 37, 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, 38, 39])
total number of confs: 504
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497368 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NC(F)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 15, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 34, 13, 1, 1, 1, 1, 1, 1, 1, 45, 60, 60, 60, 60, 60, 80, 80, 80, 201, 201, 201, 201, 201, 201, 60, 34, 34, 1, 60, 60, 60, 60, 60, 80, 201, 201, 201, 60, 60] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 435
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497368 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497368
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497368/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497368
Building REAL300025497369
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497369'
/scratch/stefan/7787277/working/building/REAL300025497369 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497369

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497369/0 /scratch/stefan/7787277/working/building/REAL300025497369 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 222)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/222
`/scratch/stefan/7787277/working/3D/222' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1)

`REAL300025497369.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497369.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497369/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497369 none CC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 6, 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, 6, 7, 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: [14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 56, 139, 139, 139, 139, 139, 1, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 27, 27, 139, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 7, 8, 9, 10, 11, 12, 13, 23, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 283
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497369 none CC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 179, 179, 179, 139, 139, 139, 139, 139, 106, 45, 106, 13, 1, 1, 1, 1, 1, 1, 1, 139, 201, 201, 201, 201, 201, 179, 139, 139, 139, 139, 139, 45, 45, 1, 139, 139] 201
rigid atoms, others: [37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 601
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497369 none CC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 14, 14, 14, 39, 39, 86, 125, 201, 201, 201, 201, 201, 14, 1, 2, 2, 2, 1, 7, 14, 14, 14, 14, 14, 86, 86, 201, 14, 14] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 517
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497369 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497369
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497369/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497369
Building REAL300025497370
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497370'
/scratch/stefan/7787277/working/building/REAL300025497370 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497370

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497370/0 /scratch/stefan/7787277/working/building/REAL300025497370 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 223)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/223
`/scratch/stefan/7787277/working/3D/223' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497370.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497370.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497370/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497370 none CN1N=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 49, 148, 148, 148, 148, 148, 1, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 17, 17, 148, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 260
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497370 none CN1N=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 199, 199, 199, 148, 148, 148, 148, 148, 125, 52, 125, 13, 1, 1, 1, 1, 1, 1, 1, 148, 201, 201, 201, 201, 201, 199, 148, 148, 148, 148, 148, 52, 52, 1, 148, 148] 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])
total number of confs: 606
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497370 none CN1N=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 24, 24, 60, 112, 201, 201, 201, 201, 201, 11, 2, 2, 2, 1, 1, 5, 11, 11, 11, 11, 11, 60, 60, 201, 11, 11] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 468
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497370 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497370
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497370/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497370
Building REAL300025497371
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497371'
/scratch/stefan/7787277/working/building/REAL300025497371 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497371

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497371/0 /scratch/stefan/7787277/working/building/REAL300025497371 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 224)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/224
`/scratch/stefan/7787277/working/3D/224' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(OC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497371.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497371.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497371/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497371 none CCC(OC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [167, 200, 97, 200, 201, 97, 97, 52, 52, 52, 52, 52, 52, 42, 52, 13, 1, 1, 1, 1, 1, 1, 1, 52, 201, 201, 201, 201, 201, 200, 201, 201, 201, 97, 52, 52, 52, 52, 52, 42, 42, 1, 52, 52] 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])
total number of confs: 1015
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497371 none CCC(OC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 26, 5, 26, 35, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 12, 52, 52, 52, 52, 52, 1, 38, 38, 38, 38, 38, 26, 35, 35, 35, 5, 1, 1, 1, 1, 1, 8, 8, 52, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 300
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497371 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497371
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497371/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497371
Building REAL300025497372
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497372'
/scratch/stefan/7787277/working/building/REAL300025497372 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497372

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497372/0 /scratch/stefan/7787277/working/building/REAL300025497372 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 225)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/225
`/scratch/stefan/7787277/working/3D/225' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497372.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497372.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497372/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497372 none COCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 161, 145, 131, 32, 32, 32, 32, 32, 32, 32, 32, 32, 26, 32, 13, 1, 1, 1, 1, 1, 1, 1, 32, 201, 201, 201, 201, 201, 161, 161, 161, 161, 131, 131, 32, 32, 32, 32, 32, 32, 26, 26, 1, 32, 32] 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])
total number of confs: 974
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: REAL300025497372 none COCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 17, 14, 10, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 32, 32, 32, 32, 32, 1, 37, 37, 37, 32, 32, 17, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 4, 4, 32, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 229
number of broken/clashed sets: 169
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497372 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497372
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497372/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497372
Building REAL300025497373
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497373'
/scratch/stefan/7787277/working/building/REAL300025497373 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497373

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497373/0 /scratch/stefan/7787277/working/building/REAL300025497373 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 226)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/226
`/scratch/stefan/7787277/working/3D/226' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497373.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497373.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497373/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497373 none CCCC(C)CC(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 175, 201, 63, 63, 63, 56, 56, 56, 56, 56, 48, 31, 48, 13, 1, 1, 1, 1, 1, 1, 1, 56, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 63, 56, 56, 56, 56, 56, 31, 31, 1, 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])
total number of confs: 824
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: REAL300025497373 none CCCC(C)CC(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 17, 27, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 56, 56, 56, 56, 56, 1, 36, 36, 36, 36, 36, 36, 36, 27, 27, 27, 27, 17, 17, 3, 1, 1, 1, 1, 1, 5, 5, 56, 1, 1] 201
rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 246
number of broken/clashed sets: 71
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497373 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497373
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497373/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497373
Building REAL300025497374
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497374'
/scratch/stefan/7787277/working/building/REAL300025497374 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497374

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497374/0 /scratch/stefan/7787277/working/building/REAL300025497374 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 227)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/227
`/scratch/stefan/7787277/working/3D/227' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497374.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497374.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497374/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497374 none COC(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 118, 118, 118, 85, 85, 85, 85, 85, 65, 28, 65, 13, 1, 1, 1, 1, 1, 1, 1, 85, 201, 201, 201, 201, 201, 201, 201, 201, 201, 118, 85, 85, 85, 85, 85, 28, 28, 1, 85, 85] 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])
total number of confs: 741
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497374 none COC(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 27, 22, 26, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 21, 85, 85, 85, 85, 85, 1, 28, 28, 28, 27, 27, 27, 27, 22, 22, 5, 1, 1, 1, 1, 1, 11, 11, 85, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 246
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497374 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497374
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497374/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497374
Building REAL300025497375
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497375'
/scratch/stefan/7787277/working/building/REAL300025497375 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497375

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497375/0 /scratch/stefan/7787277/working/building/REAL300025497375 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 228)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/228
`/scratch/stefan/7787277/working/3D/228' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1)

`REAL300025497375.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497375.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497375/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497375 none CN1C=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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: [34, 34, 34, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 24, 61, 61, 61, 61, 61, 1, 34, 34, 34, 34, 34, 34, 14, 14, 5, 1, 1, 1, 1, 1, 14, 14, 61, 1, 1, 34] 201
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 202
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497375 none CN1C=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 141, 85, 85, 85, 61, 61, 61, 61, 61, 55, 34, 55, 13, 1, 1, 1, 1, 1, 1, 1, 61, 201, 201, 201, 201, 201, 201, 141, 141, 85, 61, 61, 61, 61, 61, 34, 34, 1, 61, 61, 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])
total number of confs: 677
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497375 none CN1C=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 14, 14, 14, 34, 34, 34, 34, 34, 65, 65, 105, 137, 201, 201, 201, 201, 201, 34, 1, 1, 2, 2, 2, 1, 6, 6, 14, 34, 34, 34, 34, 34, 105, 105, 201, 34, 34, 1] 201
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: 564
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497375 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497375
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497375/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497375
Building REAL300025497376
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497376'
/scratch/stefan/7787277/working/building/REAL300025497376 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497376

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497376/0 /scratch/stefan/7787277/working/building/REAL300025497376 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 229)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/229
`/scratch/stefan/7787277/working/3D/229' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCCCC2)C1)

`REAL300025497376.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497376.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497376/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497376 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [5, 1, 5, 15, 30, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 17, 1, 15, 15, 126, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1] 201
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 14, 15, 48, 49, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 240
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497376 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [36, 17, 36, 73, 110, 201, 201, 201, 201, 201, 17, 17, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 17, 73, 73, 201, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 201
rigid atoms, others: [35, 36, 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, 48, 49])
total number of confs: 493
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497376 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [84, 45, 13, 1, 1, 1, 1, 1, 1, 1, 84, 126, 126, 126, 126, 126, 175, 175, 175, 201, 201, 201, 201, 201, 201, 126, 45, 45, 1, 126, 126, 126, 126, 126, 175, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 126, 126] 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: 650
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497376 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497376
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497376/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497376
Building REAL300025497377
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497377'
/scratch/stefan/7787277/working/building/REAL300025497377 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497377

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497377/0 /scratch/stefan/7787277/working/building/REAL300025497377 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 230)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/230
`/scratch/stefan/7787277/working/3D/230' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497377.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497377.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497377/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497377 none C=CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
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, 88, 88, 88, 83, 83, 83, 83, 83, 67, 30, 67, 13, 1, 1, 1, 1, 1, 1, 1, 83, 201, 201, 201, 201, 201, 198, 198, 88, 83, 83, 83, 83, 83, 30, 30, 1, 83, 83] 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])
total number of confs: 767
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497377 none C=CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 15, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 16, 83, 83, 83, 83, 83, 1, 25, 25, 25, 15, 15, 11, 11, 3, 1, 1, 1, 1, 1, 7, 7, 83, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 217
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497377 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497377
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497377/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497377
Building REAL300025497378
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497378'
/scratch/stefan/7787277/working/building/REAL300025497378 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497378

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497378/0 /scratch/stefan/7787277/working/building/REAL300025497378 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 231)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/231
`/scratch/stefan/7787277/working/3D/231' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COCCC2)C1)

`REAL300025497378.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497378.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497378/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497378 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 5, 7, 7, 6, 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, 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, 13, 21, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 1, 13, 13, 79, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 41, 10, 11, 12, 13, 14, 15, 42, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 161
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497378 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 5, 7, 7, 6, 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, 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: [42, 18, 42, 76, 107, 201, 201, 201, 201, 201, 18, 18, 18, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 18, 76, 76, 201, 18, 18, 18, 18, 18, 9, 1, 1, 1, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [34, 35, 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, 41, 42])
total number of confs: 508
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497378 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 12, 5, 5, 5, 5, 7, 7, 6, 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, 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: [58, 39, 13, 1, 1, 1, 1, 1, 1, 1, 58, 79, 79, 79, 79, 79, 114, 114, 114, 201, 201, 201, 201, 201, 79, 39, 39, 1, 79, 79, 79, 79, 79, 114, 201, 201, 201, 201, 201, 201, 201, 79, 79] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 506
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497378 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497378
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497378/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497378
Building REAL300025497379
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497379'
/scratch/stefan/7787277/working/building/REAL300025497379 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497379

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497379/0 /scratch/stefan/7787277/working/building/REAL300025497379 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 232)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/232
`/scratch/stefan/7787277/working/3D/232' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(=O)C1CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497379.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497379.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497379/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497379 none COC(=O)C1CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 18, 34, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 26, 60, 60, 60, 60, 60, 1, 34, 34, 34, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 16, 16, 60, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 224
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497379 none COC(=O)C1CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 151, 201, 151, 151, 68, 68, 68, 60, 60, 60, 60, 60, 56, 36, 56, 13, 1, 1, 1, 1, 1, 1, 1, 60, 201, 201, 201, 151, 151, 151, 151, 68, 60, 60, 60, 60, 60, 36, 36, 1, 60, 60] 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])
total number of confs: 649
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497379 none COC(=O)C1CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 8, 8, 8, 18, 18, 18, 18, 18, 39, 39, 69, 100, 151, 151, 151, 151, 151, 18, 4, 4, 4, 1, 1, 1, 1, 8, 18, 18, 18, 18, 18, 69, 69, 151, 18, 18] 201
rigid atoms, others: [32, 2, 4, 5, 6, 7, 29, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 424
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497379 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497379
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497379/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497379
Building REAL300025497380
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497380'
/scratch/stefan/7787277/working/building/REAL300025497380 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497380

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497380/0 /scratch/stefan/7787277/working/building/REAL300025497380 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 233)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/233
`/scratch/stefan/7787277/working/3D/233' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCOC2)C1)

`REAL300025497380.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497380.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497380/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497380 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCOC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 1, 13, 13, 77, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1] 201
rigid atoms, others: [32, 1, 43, 44, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 178
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497380 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCOC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 17, 42, 83, 114, 201, 201, 201, 201, 201, 17, 17, 17, 17, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 17, 83, 83, 201, 17, 17, 17, 17, 17, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 201
rigid atoms, others: [34, 35, 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, 43, 44])
total number of confs: 522
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497380 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCOC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 77, 77, 77, 77, 77, 115, 115, 115, 201, 201, 201, 201, 201, 77, 32, 32, 1, 77, 77, 77, 77, 77, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 660
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497380 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497380
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497380/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497380
Building REAL300025497381
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497381'
/scratch/stefan/7787277/working/building/REAL300025497381 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497381

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497381/0 /scratch/stefan/7787277/working/building/REAL300025497381 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 234)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/234
`/scratch/stefan/7787277/working/3D/234' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497381.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497381.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497381/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497381 none CCOCCC(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  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, 129, 129, 129, 79, 79, 79, 79, 79, 60, 30, 60, 13, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 201, 201, 199, 199, 129, 79, 79, 79, 79, 79, 30, 30, 1, 79, 79] 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])
total number of confs: 784
number of broken/clashed sets: 80
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497381 none CCOCCC(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 20, 18, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 18, 79, 79, 79, 79, 79, 1, 26, 26, 26, 26, 26, 20, 20, 18, 18, 5, 1, 1, 1, 1, 1, 9, 9, 79, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 207
number of broken/clashed sets: 80
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497381 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497381
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497381/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497381
Building REAL300025497382
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497382'
/scratch/stefan/7787277/working/building/REAL300025497382 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497382

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497382/0 /scratch/stefan/7787277/working/building/REAL300025497382 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 235)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/235
`/scratch/stefan/7787277/working/3D/235' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCNC(=O)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497382.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497382.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497382/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497382 none CCNC(=O)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 190, 190, 182, 190, 182, 111, 111, 111, 88, 88, 88, 88, 88, 60, 29, 60, 13, 1, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 201, 201, 190, 182, 182, 182, 182, 111, 88, 88, 88, 88, 88, 29, 29, 1, 88, 88] 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])
total number of confs: 773
number of broken/clashed sets: 93
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497382 none CCNC(=O)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 21, 21, 12, 21, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 19, 88, 88, 88, 88, 88, 1, 33, 33, 33, 33, 33, 21, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 10, 10, 88, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 275
number of broken/clashed sets: 93
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497382 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497382
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497382/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497382
Building REAL300025497383
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497383'
/scratch/stefan/7787277/working/building/REAL300025497383 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497383

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497383/0 /scratch/stefan/7787277/working/building/REAL300025497383 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 236)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/236
`/scratch/stefan/7787277/working/3D/236' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC=N2)C1)

`REAL300025497383.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497383.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497383/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497383 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 14, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 20, 47, 144, 144, 144, 144, 144, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 1, 20, 20, 144, 1, 1, 1, 1, 1, 6, 10, 10, 1, 1] 201
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34])
total number of confs: 267
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497383 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 14, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 10, 25, 58, 103, 201, 201, 201, 201, 201, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 10, 58, 58, 201, 10, 10, 10, 10, 10, 3, 1, 1, 10, 10] 201
rigid atoms, others: [33, 34, 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, 35, 36])
total number of confs: 444
number of broken/clashed sets: 37
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497383 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 14, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 50, 13, 1, 1, 1, 1, 1, 1, 1, 113, 144, 144, 144, 144, 144, 201, 201, 201, 201, 201, 201, 201, 144, 50, 50, 1, 144, 144, 144, 144, 144, 201, 201, 201, 144, 144] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 625
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497383 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497383
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497383/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497383
Building REAL300025497384
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497384'
/scratch/stefan/7787277/working/building/REAL300025497384 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497384

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497384/0 /scratch/stefan/7787277/working/building/REAL300025497384 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 237)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/237
`/scratch/stefan/7787277/working/3D/237' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497384.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497384.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497384/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497384 none COCC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 136, 201, 136, 136, 92, 92, 92, 92, 92, 66, 29, 66, 13, 1, 1, 1, 1, 1, 1, 1, 92, 201, 201, 201, 201, 201, 201, 201, 201, 201, 136, 92, 92, 92, 92, 92, 29, 29, 1, 92, 92] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43])
total number of confs: 742
number of broken/clashed sets: 93
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497384 none COCC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 13, 5, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 92, 92, 92, 92, 92, 1, 23, 23, 23, 19, 19, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 10, 10, 92, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 219
number of broken/clashed sets: 93
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497384 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497384
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497384/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497384
Building REAL300025497385
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497385'
/scratch/stefan/7787277/working/building/REAL300025497385 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497385

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497385/0 /scratch/stefan/7787277/working/building/REAL300025497385 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 238)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/238
`/scratch/stefan/7787277/working/3D/238' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497385.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497385.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497385/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497385 none CC(C)(C)CCCC(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 174, 201, 174, 198, 74, 74, 74, 45, 45, 45, 45, 45, 39, 26, 39, 12, 1, 1, 1, 1, 1, 1, 1, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 74, 45, 45, 45, 45, 45, 26, 26, 1, 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])
total number of confs: 1125
number of broken/clashed sets: 51
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497385 none CC(C)(C)CCCC(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [39, 39, 33, 39, 33, 25, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 10, 45, 45, 45, 45, 45, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 25, 25, 5, 1, 1, 1, 1, 1, 6, 6, 45, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49])
total number of confs: 309
number of broken/clashed sets: 51
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497385 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497385
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497385/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497385
Building REAL300025497386
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497386'
/scratch/stefan/7787277/working/building/REAL300025497386 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497386

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497386/0 /scratch/stefan/7787277/working/building/REAL300025497386 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 239)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/239
`/scratch/stefan/7787277/working/3D/239' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497386.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497386.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497386/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497386 none C=CCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
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, 144, 56, 56, 56, 46, 46, 46, 46, 46, 46, 31, 46, 13, 1, 1, 1, 1, 1, 1, 1, 46, 201, 201, 201, 201, 201, 144, 144, 56, 46, 46, 46, 46, 46, 31, 31, 1, 46, 46] 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])
total number of confs: 834
number of broken/clashed sets: 167
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497386 none C=CCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 14, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 46, 46, 46, 46, 46, 1, 37, 37, 37, 30, 30, 8, 8, 3, 1, 1, 1, 1, 1, 5, 5, 46, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 203
number of broken/clashed sets: 167
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497386 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497386
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497386/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497386
Building REAL300025497387
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497387'
/scratch/stefan/7787277/working/building/REAL300025497387 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497387

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497387/0 /scratch/stefan/7787277/working/building/REAL300025497387 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 240)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/240
`/scratch/stefan/7787277/working/3D/240' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COC=N2)C1)

`REAL300025497387.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497387.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497387/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497387 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 22, 50, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 1, 22, 22, 147, 1, 1, 1, 1, 1, 6, 9, 9, 1, 1] 201
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34])
total number of confs: 272
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497387 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 9, 24, 56, 102, 201, 201, 201, 201, 201, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 9, 56, 56, 201, 9, 9, 9, 9, 9, 3, 1, 1, 9, 9] 201
rigid atoms, others: [33, 34, 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, 35, 36])
total number of confs: 437
number of broken/clashed sets: 40
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497387 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 52, 13, 1, 1, 1, 1, 1, 1, 1, 112, 147, 147, 147, 147, 147, 201, 201, 201, 201, 201, 201, 201, 147, 52, 52, 1, 147, 147, 147, 147, 147, 201, 201, 201, 147, 147] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 617
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497387 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497387
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497387/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497387
Building REAL300025497388
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497388'
/scratch/stefan/7787277/working/building/REAL300025497388 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497388

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497388/0 /scratch/stefan/7787277/working/building/REAL300025497388 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 241)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/241
`/scratch/stefan/7787277/working/3D/241' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2CCC(=O)N2)C1)

`REAL300025497388.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497388.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497388/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497388 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2CCC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 18, 35, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 1, 18, 18, 125, 1, 1, 1, 1, 1, 4, 15, 15, 15, 15, 15, 1, 1] 201
rigid atoms, others: [32, 1, 33, 40, 41, 10, 11, 12, 13, 14, 15, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39])
total number of confs: 244
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497388 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2CCC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 15, 41, 74, 111, 201, 201, 201, 201, 201, 15, 15, 15, 15, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 15, 74, 74, 201, 15, 15, 15, 15, 15, 10, 1, 1, 1, 1, 1, 15, 15] 201
rigid atoms, others: [35, 36, 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, 40, 41])
total number of confs: 478
number of broken/clashed sets: 34
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497388 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2CCC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 47, 12, 1, 1, 1, 1, 1, 1, 1, 90, 125, 125, 125, 125, 125, 171, 171, 171, 201, 201, 201, 201, 201, 201, 125, 47, 47, 1, 125, 125, 125, 125, 125, 171, 201, 201, 201, 201, 201, 125, 125] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 630
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497388 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497388
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497388/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497388
Building REAL300025497389
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497389'
/scratch/stefan/7787277/working/building/REAL300025497389 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497389

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497389/0 /scratch/stefan/7787277/working/building/REAL300025497389 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 242)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/242
`/scratch/stefan/7787277/working/3D/242' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497389.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497389.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497389/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497389 none O=C(CC1=CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 22, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 63, 63, 63, 63, 63, 1, 22, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 5, 1, 1, 1, 1, 1, 7, 7, 63, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 192
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497389 none O=C(CC1=CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 200, 201, 201, 201, 201, 201, 63, 63, 63, 63, 63, 48, 29, 48, 13, 1, 1, 1, 1, 1, 1, 1, 63, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 102, 63, 63, 63, 63, 63, 29, 29, 1, 63, 63] 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])
total number of confs: 778
number of broken/clashed sets: 66
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497389 none O=C(CC1=CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 1, 20, 20, 36, 36, 36, 36, 36, 46, 46, 86, 131, 201, 201, 201, 201, 201, 36, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 36, 36, 36, 36, 36, 86, 86, 201, 36, 36] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 545
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497389 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497389
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497389/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497389
Building REAL300025497390
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497390'
/scratch/stefan/7787277/working/building/REAL300025497390 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497390

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497390/0 /scratch/stefan/7787277/working/building/REAL300025497390 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 243)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/243
`/scratch/stefan/7787277/working/3D/243' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N1)

`REAL300025497390.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497390.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497390/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497390 none CC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 33, 56, 152, 152, 152, 152, 152, 1, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 33, 33, 152, 1, 1, 14] 201
rigid atoms, others: [32, 33, 34, 38, 7, 8, 9, 10, 11, 12, 13, 23, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40])
total number of confs: 313
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497390 none CC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 193, 193, 193, 152, 152, 152, 152, 152, 109, 45, 109, 13, 1, 1, 1, 1, 1, 1, 1, 151, 201, 201, 201, 201, 201, 193, 152, 152, 152, 152, 152, 45, 45, 1, 152, 152, 201] 201
rigid atoms, others: [37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 601
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497390 none CC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 14, 40, 40, 100, 132, 201, 201, 201, 201, 201, 14, 1, 2, 2, 2, 1, 5, 14, 14, 14, 14, 14, 100, 100, 201, 14, 14, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 24, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 560
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497390 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497390
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497390/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497390
Building REAL300025497391
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497391'
/scratch/stefan/7787277/working/building/REAL300025497391 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497391

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497391/0 /scratch/stefan/7787277/working/building/REAL300025497391 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 244)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/244
`/scratch/stefan/7787277/working/3D/244' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSCC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497391.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497391.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497391/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497391 none CSCC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 197, 194, 118, 194, 118, 118, 89, 89, 89, 89, 89, 63, 30, 63, 13, 1, 1, 1, 1, 1, 1, 1, 89, 201, 201, 201, 197, 197, 194, 194, 194, 194, 118, 89, 89, 89, 89, 89, 30, 30, 1, 89, 89] 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])
total number of confs: 785
number of broken/clashed sets: 89
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497391 none CSCC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [32, 16, 13, 4, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 89, 89, 89, 89, 89, 1, 32, 32, 32, 16, 16, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 9, 9, 89, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 217
number of broken/clashed sets: 89
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497391 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497391
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497391/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497391
Building REAL300025497392
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497392'
/scratch/stefan/7787277/working/building/REAL300025497392 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025497392

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497392/0 /scratch/stefan/7787277/working/building/REAL300025497392 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 245)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/245
`/scratch/stefan/7787277/working/3D/245' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497392.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497392.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497392/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497392 none C[N@@H+]1CCCC1C(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
4  conformations in input
total number of sets (complete confs): 4
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 3, 4, 4, 4, 4, 4, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 4, 1, 1] 4
rigid atoms, others: [45, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 16, 17, 46, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 17
number of broken/clashed sets: 0
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497392 none C[N@@H+]1CCCC1C(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
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, 4, 4, 4, 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
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])
total number of confs: 5
number of broken/clashed sets: 0
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497392 none C[N@@H+]1CCCC1C(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
4  conformations in input
total number of sets (complete confs): 4
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 4, 4, 4, 3, 3] 4
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 33, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 21
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497392 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497392/1 /scratch/stefan/7787277/working/building/REAL300025497392 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 246)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/246
`/scratch/stefan/7787277/working/3D/246' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497392.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497392.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497392/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497392 none C[N@H+]1CCCC1C(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 10, 26, 26, 26, 26, 26, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 9, 9, 26, 1, 1] 29
rigid atoms, others: [45, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 63
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497392 none C[N@H+]1CCCC1C(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 29, 29, 26, 26, 26, 26, 26, 25, 22, 25, 13, 1, 1, 1, 1, 1, 1, 1, 26, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 26, 26, 26, 26, 26, 22, 22, 1, 26, 26] 29
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])
total number of confs: 88
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497392 none C[N@H+]1CCCC1C(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 8, 8, 16, 18, 29, 29, 29, 29, 29, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 16, 16, 29, 5, 5] 29
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 33, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 89
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497392 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `2'
/scratch/stefan/7787277/working/building/REAL300025497392/2 /scratch/stefan/7787277/working/building/REAL300025497392 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 2 (index: 247)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/247
`/scratch/stefan/7787277/working/3D/247' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497392.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025497392.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497392/2/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: REAL300025497392 none CN1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [6, 6, 6, 6, 6, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 53, 155, 155, 155, 155, 155, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 1, 1, 1, 25, 25, 155, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 290
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497392 none CN1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 155, 155, 155, 155, 155, 117, 53, 117, 13, 1, 1, 1, 1, 1, 1, 1, 155, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 155, 155, 155, 155, 155, 53, 53, 1, 155, 155] 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])
total number of confs: 620
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497392 none CN1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 6, 6, 6, 6, 6, 21, 21, 56, 102, 201, 201, 201, 201, 201, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 56, 56, 201, 6, 6] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 454
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497392 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497392
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497392/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497392/1.*
2: /scratch/stefan/7787277/working/building/REAL300025497392/2.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497392
Building REAL300025497393
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497393'
/scratch/stefan/7787277/working/building/REAL300025497393 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497393

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497393/0 /scratch/stefan/7787277/working/building/REAL300025497393 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 248)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/248
`/scratch/stefan/7787277/working/3D/248' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497393.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497393.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497393/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497393 none CCC(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 151, 151, 151, 151, 71, 71, 71, 71, 71, 71, 71, 71, 51, 29, 51, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 151, 151, 151, 71, 71, 71, 71, 71, 71, 29, 29, 1, 71, 71] 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])
total number of confs: 853
number of broken/clashed sets: 108
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497393 none CCC(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 14, 71, 71, 71, 71, 71, 1, 41, 41, 41, 41, 41, 11, 11, 11, 2, 1, 1, 1, 1, 1, 7, 7, 71, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 260
number of broken/clashed sets: 108
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497393 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497393
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497393/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497393
Building REAL300025497394
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497394'
/scratch/stefan/7787277/working/building/REAL300025497394 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497394

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497394/0 /scratch/stefan/7787277/working/building/REAL300025497394 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 249)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/249
`/scratch/stefan/7787277/working/3D/249' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C=CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497394.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497394.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497394/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497394 none CC(C)(C)C=CC(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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, 97, 97, 97, 79, 79, 79, 79, 79, 64, 40, 64, 13, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 97, 79, 79, 79, 79, 79, 40, 40, 1, 79, 79] 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])
total number of confs: 645
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: REAL300025497394 none CC(C)(C)C=CC(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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: [21, 21, 21, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 30, 79, 79, 79, 79, 79, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 17, 17, 79, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 209
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497394 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497394
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497394/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497394
Building REAL300025497395
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497395'
/scratch/stefan/7787277/working/building/REAL300025497395 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497395

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497395/0 /scratch/stefan/7787277/working/building/REAL300025497395 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 250)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/250
`/scratch/stefan/7787277/working/3D/250' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)N=C2)C1)

`REAL300025497395.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497395.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497395/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497395 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 15, 8, 1, 5, 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, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 14, 30, 98, 98, 98, 98, 98, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 15, 1, 14, 14, 98, 1, 1, 1, 1, 1, 5, 15, 15, 15, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37])
total number of confs: 197
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497395 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 15, 8, 1, 5, 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, 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: [38, 15, 38, 76, 123, 201, 201, 201, 201, 201, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 76, 76, 201, 15, 15, 15, 15, 15, 5, 1, 1, 1, 15, 15] 201
rigid atoms, others: [35, 36, 37, 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, 38, 39])
total number of confs: 518
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497395 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 15, 8, 1, 5, 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, 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: [69, 43, 13, 1, 1, 1, 1, 1, 1, 1, 69, 98, 98, 98, 98, 98, 141, 141, 141, 201, 201, 201, 201, 201, 201, 98, 43, 43, 1, 98, 98, 98, 98, 98, 141, 201, 201, 201, 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])
total number of confs: 559
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497395 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497395
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497395/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497395
Building REAL300025497396
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497396'
/scratch/stefan/7787277/working/building/REAL300025497396 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497396

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497396/0 /scratch/stefan/7787277/working/building/REAL300025497396 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 251)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/251
`/scratch/stefan/7787277/working/3D/251' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497396.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497396.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497396/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497396 none COCCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
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, 152, 102, 34, 34, 34, 32, 32, 32, 32, 32, 32, 24, 32, 13, 1, 1, 1, 1, 1, 1, 1, 32, 201, 201, 201, 201, 201, 190, 190, 102, 102, 34, 32, 32, 32, 32, 32, 24, 24, 1, 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])
total number of confs: 754
number of broken/clashed sets: 159
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497396 none COCCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 29, 18, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 32, 32, 32, 32, 32, 1, 37, 37, 37, 37, 37, 29, 29, 9, 9, 3, 1, 1, 1, 1, 1, 4, 4, 32, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 190
number of broken/clashed sets: 159
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497396 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497396
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497396/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497396
Building REAL300025497397
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497397'
/scratch/stefan/7787277/working/building/REAL300025497397 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497397

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497397/0 /scratch/stefan/7787277/working/building/REAL300025497397 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 252)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/252
`/scratch/stefan/7787277/working/3D/252' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497397.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497397.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497397/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497397 none CCCC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 201, 174, 89, 174, 89, 89, 59, 59, 59, 59, 59, 46, 28, 46, 13, 1, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 201, 201, 174, 174, 174, 174, 89, 59, 59, 59, 59, 59, 28, 28, 1, 59, 59] 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])
total number of confs: 837
number of broken/clashed sets: 57
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497397 none CCCC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [37, 37, 21, 5, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 16, 59, 59, 59, 59, 59, 1, 37, 37, 37, 37, 37, 37, 37, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 8, 8, 59, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 252
number of broken/clashed sets: 57
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497397 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497397
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497397/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497397
Building REAL300025497398
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497398'
/scratch/stefan/7787277/working/building/REAL300025497398 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497398

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497398/0 /scratch/stefan/7787277/working/building/REAL300025497398 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 253)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/253
`/scratch/stefan/7787277/working/3D/253' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497398.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497398.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497398/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497398 none CC1=NN(C)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 46, 132, 132, 132, 132, 132, 1, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 26, 26, 132, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 275
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497398 none CC1=NN(C)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 132, 132, 132, 132, 132, 99, 42, 99, 13, 1, 1, 1, 1, 1, 1, 1, 132, 201, 201, 201, 201, 201, 201, 201, 184, 132, 132, 132, 132, 132, 42, 42, 1, 132, 132] 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])
total number of confs: 599
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497398 none CC1=NN(C)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 15, 15, 15, 15, 15, 43, 43, 97, 129, 201, 201, 201, 201, 201, 15, 2, 2, 2, 2, 2, 2, 1, 8, 15, 15, 15, 15, 15, 97, 97, 201, 15, 15] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 568
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497398 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497398
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497398/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497398
Building REAL300025497399
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497399'
/scratch/stefan/7787277/working/building/REAL300025497399 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497399

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497399/0 /scratch/stefan/7787277/working/building/REAL300025497399 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 254)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/254
`/scratch/stefan/7787277/working/3D/254' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3CCC2O3)C1)

`REAL300025497399.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497399.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497399/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497399 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3CCC2O3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 7, 7, 6, 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, 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, 18, 40, 127, 127, 127, 127, 127, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 12, 1, 18, 18, 127, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1] 201
rigid atoms, others: [32, 1, 45, 33, 44, 10, 11, 12, 13, 14, 15, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 243
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497399 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3CCC2O3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 7, 7, 6, 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, 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: [34, 12, 34, 70, 111, 201, 201, 201, 201, 201, 12, 12, 12, 12, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 12, 70, 70, 201, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 201
rigid atoms, others: [35, 36, 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, 44, 45])
total number of confs: 467
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497399 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3CCC2O3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 12, 5, 7, 7, 6, 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, 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: [95, 45, 13, 1, 1, 1, 1, 1, 1, 1, 95, 127, 127, 127, 127, 127, 177, 177, 177, 201, 201, 201, 201, 201, 201, 127, 45, 45, 1, 127, 127, 127, 127, 127, 177, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127] 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: 630
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497399 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497399
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497399/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497399
Building REAL300025497400
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497400'
/scratch/stefan/7787277/working/building/REAL300025497400 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497400

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497400/0 /scratch/stefan/7787277/working/building/REAL300025497400 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 255)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/255
`/scratch/stefan/7787277/working/3D/255' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1)

`REAL300025497400.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497400.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497400/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497400 none CC1=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 20, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 23, 90, 90, 90, 90, 90, 1, 27, 27, 27, 27, 27, 27, 20, 20, 4, 1, 1, 1, 1, 1, 14, 14, 90, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 231
number of broken/clashed sets: 55
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497400 none CC1=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 116, 116, 116, 90, 90, 90, 90, 90, 52, 29, 52, 13, 1, 1, 1, 1, 1, 1, 1, 90, 201, 201, 201, 201, 201, 201, 201, 201, 116, 90, 90, 90, 90, 90, 29, 29, 1, 90, 90] 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])
total number of confs: 748
number of broken/clashed sets: 55
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497400 none CC1=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 14, 14, 14, 27, 27, 27, 27, 27, 47, 47, 81, 120, 201, 201, 201, 201, 201, 27, 1, 1, 2, 2, 2, 1, 5, 5, 14, 27, 27, 27, 27, 27, 81, 81, 201, 27, 27] 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: 548
number of broken/clashed sets: 55
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497400 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497400
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497400/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497400
Building REAL300025497401
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497401'
/scratch/stefan/7787277/working/building/REAL300025497401 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497401

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497401/0 /scratch/stefan/7787277/working/building/REAL300025497401 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 256)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/256
`/scratch/stefan/7787277/working/3D/256' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1)

`REAL300025497401.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497401.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497401/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497401 none CCN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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: [24, 11, 11, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 26, 77, 77, 77, 77, 77, 1, 11, 11, 24, 24, 24, 24, 24, 11, 4, 1, 1, 1, 1, 1, 15, 15, 77, 1, 1, 11] 201
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497401 none CCN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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, 145, 145, 145, 85, 85, 85, 77, 77, 77, 77, 77, 68, 38, 68, 13, 1, 1, 1, 1, 1, 1, 1, 77, 145, 145, 201, 201, 201, 201, 201, 145, 85, 77, 77, 77, 77, 77, 38, 38, 1, 77, 77, 145] 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: 724
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497401 none CCN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 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: [5, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 27, 27, 48, 68, 145, 145, 145, 145, 145, 11, 1, 1, 5, 5, 5, 5, 5, 1, 5, 11, 11, 11, 11, 11, 48, 48, 145, 11, 11, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 43, 24, 25, 31] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 349
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497401 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497401
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497401/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497401
Building REAL300025497402
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497402'
/scratch/stefan/7787277/working/building/REAL300025497402 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497402

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497402/0 /scratch/stefan/7787277/working/building/REAL300025497402 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 257)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/257
`/scratch/stefan/7787277/working/3D/257' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC1=NC=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497402.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497402.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497402/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497402 none NC1=NC=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [8, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 52, 140, 140, 140, 140, 140, 1, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 27, 27, 140, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 288
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497402 none NC1=NC=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [8, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 196, 196, 196, 140, 140, 140, 140, 140, 105, 40, 105, 13, 1, 1, 1, 1, 1, 1, 1, 140, 201, 201, 201, 201, 196, 140, 140, 140, 140, 140, 40, 40, 1, 140, 140] 201
rigid atoms, others: [38, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 612
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497402 none NC1=NC=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [8, 1, 8, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 13, 13, 13, 13, 13, 34, 34, 80, 126, 201, 201, 201, 201, 201, 13, 2, 2, 1, 1, 5, 13, 13, 13, 13, 13, 80, 80, 201, 13, 13] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 28, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 523
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497402 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497402
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497402/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497402
Building REAL300025497403
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497403'
/scratch/stefan/7787277/working/building/REAL300025497403 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497403

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497403/0 /scratch/stefan/7787277/working/building/REAL300025497403 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 258)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/258
`/scratch/stefan/7787277/working/3D/258' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497403.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497403.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497403/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497403 none O=C(CCC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 24, 28, 47, 47, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 10, 37, 37, 37, 37, 37, 1, 24, 24, 30, 30, 47, 47, 47, 47, 47, 5, 1, 1, 1, 1, 1, 6, 6, 37, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 244
number of broken/clashed sets: 51
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497403 none O=C(CCC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 146, 148, 201, 201, 37, 37, 37, 37, 37, 36, 26, 36, 12, 1, 1, 1, 1, 1, 1, 1, 37, 146, 146, 148, 148, 201, 201, 201, 201, 201, 57, 37, 37, 37, 37, 37, 26, 26, 1, 37, 37] 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])
total number of confs: 789
number of broken/clashed sets: 51
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497403 none O=C(CCC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 7, 3, 1, 1, 1, 1, 27, 27, 47, 47, 47, 47, 47, 52, 52, 99, 140, 201, 201, 201, 201, 201, 47, 7, 7, 3, 3, 1, 1, 1, 1, 1, 27, 47, 47, 47, 47, 47, 99, 99, 201, 47, 47] 201
rigid atoms, others: [32, 3, 4, 5, 6, 28, 29, 30, 31] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 595
number of broken/clashed sets: 51
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497403 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497403
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497403/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497403
Building REAL300025497404
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497404'
/scratch/stefan/7787277/working/building/REAL300025497404 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497404

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497404/0 /scratch/stefan/7787277/working/building/REAL300025497404 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 259)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/259
`/scratch/stefan/7787277/working/3D/259' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1)

`REAL300025497404.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497404.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497404/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497404 none CC1=C(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.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, 1, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 31, 51, 134, 134, 134, 134, 134, 1, 12, 12, 12, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 31, 31, 134, 1, 1, 12] 201
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 283
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497404 none CC1=C(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.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, 1, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 134, 134, 134, 134, 134, 105, 45, 105, 13, 1, 1, 1, 1, 1, 1, 1, 134, 201, 201, 201, 201, 201, 201, 201, 201, 196, 134, 134, 134, 134, 134, 45, 45, 1, 134, 134, 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])
total number of confs: 621
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497404 none CC1=C(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.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, 1, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 3, 3, 12, 12, 12, 12, 12, 38, 38, 97, 128, 201, 201, 201, 201, 201, 12, 1, 1, 2, 2, 2, 2, 2, 2, 3, 12, 12, 12, 12, 12, 97, 97, 201, 12, 12, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 559
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497404 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497404/1 /scratch/stefan/7787277/working/building/REAL300025497404 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 260)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/260
`/scratch/stefan/7787277/working/3D/260' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1C)

`REAL300025497404.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497404.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497404/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497404 none CC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', '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, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 30, 69, 69, 69, 69, 69, 1, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 17, 17, 69, 1, 1, 20, 20, 20] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 40, 23, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43])
total number of confs: 172
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497404 none CC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', '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, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 86, 86, 86, 69, 69, 69, 69, 69, 57, 37, 57, 13, 1, 1, 1, 1, 1, 1, 1, 69, 201, 201, 201, 201, 201, 201, 86, 69, 69, 69, 69, 69, 37, 37, 1, 69, 69, 201, 201, 201] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43])
total number of confs: 453
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497404 none CC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', '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, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 20, 20, 20, 20, 20, 46, 46, 90, 133, 201, 201, 201, 201, 201, 20, 1, 1, 2, 2, 2, 1, 8, 20, 20, 20, 20, 20, 90, 90, 201, 20, 20, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 540
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497404 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497404
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497404/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497404/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497404
Building REAL300025497405
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497405'
/scratch/stefan/7787277/working/building/REAL300025497405 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497405

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497405/0 /scratch/stefan/7787277/working/building/REAL300025497405 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 261)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/261
`/scratch/stefan/7787277/working/3D/261' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497405.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497405.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497405/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497405 none O=C(CC1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 29, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 11, 50, 50, 50, 50, 50, 1, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 6, 6, 50, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 248
number of broken/clashed sets: 55
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497405 none O=C(CC1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [84, 84, 84, 192, 201, 201, 201, 201, 201, 50, 50, 50, 50, 50, 42, 28, 42, 13, 1, 1, 1, 1, 1, 1, 1, 50, 192, 192, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 50, 50, 50, 50, 50, 28, 28, 1, 50, 50] 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])
total number of confs: 783
number of broken/clashed sets: 55
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497405 none O=C(CC1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 5, 1, 1, 1, 1, 1, 1, 1, 22, 22, 50, 50, 50, 50, 50, 59, 59, 95, 133, 201, 201, 201, 201, 201, 50, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 95, 95, 201, 50, 50] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 555
number of broken/clashed sets: 55
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497405 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497405
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497405/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497405
Building REAL300025497406
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497406'
/scratch/stefan/7787277/working/building/REAL300025497406 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497406

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497406/0 /scratch/stefan/7787277/working/building/REAL300025497406 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 262)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/262
`/scratch/stefan/7787277/working/3D/262' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497406.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497406.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497406/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497406 none CCCCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 104, 91, 83, 44, 44, 44, 44, 44, 44, 44, 44, 35, 24, 35, 13, 1, 1, 1, 1, 1, 1, 1, 44, 201, 201, 201, 201, 201, 201, 201, 104, 104, 83, 83, 44, 44, 44, 44, 44, 44, 24, 24, 1, 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])
total number of confs: 842
number of broken/clashed sets: 130
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497406 none CCCCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [38, 38, 19, 11, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 15, 44, 44, 44, 44, 44, 1, 38, 38, 38, 38, 38, 38, 38, 19, 19, 6, 6, 2, 1, 1, 1, 1, 1, 7, 7, 44, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 239
number of broken/clashed sets: 130
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497406 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497406
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497406/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497406
Building REAL300025497407
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497407'
/scratch/stefan/7787277/working/building/REAL300025497407 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497407

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497407/0 /scratch/stefan/7787277/working/building/REAL300025497407 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 263)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/263
`/scratch/stefan/7787277/working/3D/263' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=NOC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497407.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497407.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497407/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497407 none O=C(CC1=NOC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 8, 12, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 22, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 25, 97, 97, 97, 97, 97, 1, 22, 22, 25, 25, 5, 1, 1, 1, 1, 1, 15, 15, 97, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 39, 8, 9, 10, 11, 12, 13, 14, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 240
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497407 none O=C(CC1=NOC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 8, 12, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 200, 201, 201, 201, 201, 97, 97, 97, 97, 97, 57, 29, 57, 13, 1, 1, 1, 1, 1, 1, 1, 97, 200, 200, 201, 201, 125, 97, 97, 97, 97, 97, 29, 29, 1, 97, 97] 201
rigid atoms, others: [37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 738
number of broken/clashed sets: 38
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497407 none O=C(CC1=NOC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 8, 12, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 4, 1, 1, 1, 1, 1, 1, 12, 12, 25, 25, 25, 25, 25, 58, 58, 93, 130, 201, 201, 201, 201, 201, 25, 4, 4, 1, 1, 12, 25, 25, 25, 25, 25, 93, 93, 201, 25, 25] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 548
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497407 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497407
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497407/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497407
Building REAL300025497408
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497408'
/scratch/stefan/7787277/working/building/REAL300025497408 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497408

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497408/0 /scratch/stefan/7787277/working/building/REAL300025497408 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 264)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/264
`/scratch/stefan/7787277/working/3D/264' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=CO1)

`REAL300025497408.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497408.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497408/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497408 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.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, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 12, 7, 7, 7, 7, 7, 6, 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: [23, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 34, 129, 128, 129, 129, 129, 1, 12, 12, 12, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 1, 16, 16, 129, 1, 1, 12] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42])
total number of confs: 286
number of broken/clashed sets: 41
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497408 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.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, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 12, 7, 7, 7, 7, 7, 6, 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, 189, 189, 175, 175, 175, 129, 129, 129, 129, 129, 76, 31, 76, 13, 1, 1, 1, 1, 1, 1, 1, 129, 189, 189, 189, 201, 201, 201, 201, 201, 175, 129, 129, 129, 129, 129, 31, 31, 1, 129, 129, 189] 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: 602
number of broken/clashed sets: 41
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497408 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.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, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 12, 7, 7, 7, 7, 7, 6, 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: [4, 1, 1, 1, 1, 3, 3, 3, 12, 12, 12, 12, 12, 27, 27, 51, 84, 189, 189, 189, 189, 189, 12, 1, 1, 1, 4, 4, 4, 4, 4, 3, 12, 12, 12, 12, 12, 51, 51, 189, 12, 12, 1] 201
rigid atoms, others: [1, 2, 3, 4, 42, 23, 24, 25] set([0, 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: 409
number of broken/clashed sets: 41
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497408 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497408
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497408/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497408
Building REAL300025497409
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497409'
/scratch/stefan/7787277/working/building/REAL300025497409 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497409

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497409/0 /scratch/stefan/7787277/working/building/REAL300025497409 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 265)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/265
`/scratch/stefan/7787277/working/3D/265' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCOC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497409.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497409.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497409/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497409 none O=C(CC1CCOC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 12, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 14, 56, 56, 56, 56, 56, 1, 27, 27, 42, 42, 42, 42, 42, 42, 42, 5, 1, 1, 1, 1, 1, 7, 7, 56, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 228
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497409 none O=C(CC1CCOC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 12, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [86, 86, 86, 200, 201, 201, 201, 201, 56, 56, 56, 56, 56, 46, 29, 46, 13, 1, 1, 1, 1, 1, 1, 1, 56, 200, 200, 201, 201, 201, 201, 201, 201, 201, 86, 56, 56, 56, 56, 56, 29, 29, 1, 56, 56] 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])
total number of confs: 768
number of broken/clashed sets: 61
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497409 none O=C(CC1CCOC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 12, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 5, 1, 1, 1, 1, 1, 1, 22, 22, 42, 42, 42, 42, 42, 50, 50, 95, 139, 201, 201, 201, 201, 201, 42, 5, 5, 1, 1, 1, 1, 1, 1, 1, 22, 42, 42, 42, 42, 42, 95, 95, 201, 42, 42] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 27, 28, 29, 30, 31] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 570
number of broken/clashed sets: 61
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497409 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497409
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497409/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497409
Building REAL300025497410
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497410'
/scratch/stefan/7787277/working/building/REAL300025497410 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497410

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497410/0 /scratch/stefan/7787277/working/building/REAL300025497410 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 266)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/266
`/scratch/stefan/7787277/working/3D/266' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC=CC2)C1)

`REAL300025497410.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497410.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497410/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497410 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC=CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 19, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 5, 5, 5, 20, 20, 20, 20, 1, 13, 13, 72, 1, 1, 1, 1, 1, 5, 20, 20, 20, 20, 20, 20, 20, 1, 1] 201
rigid atoms, others: [1, 40, 41, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 169
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497410 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC=CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 20, 42, 83, 108, 201, 201, 201, 201, 201, 20, 20, 20, 20, 9, 9, 1, 9, 1, 1, 1, 1, 1, 20, 83, 83, 201, 20, 20, 20, 20, 20, 9, 1, 1, 1, 1, 1, 1, 1, 20, 20] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 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, 40, 41])
total number of confs: 514
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497410 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC=CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 1, 1, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 37, 13, 1, 1, 1, 1, 1, 1, 1, 56, 72, 72, 72, 72, 72, 97, 97, 97, 201, 201, 201, 201, 72, 37, 37, 1, 72, 72, 72, 72, 72, 97, 201, 201, 201, 201, 201, 201, 201, 72, 72] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 635
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497410 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497410
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497410/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497410
Building REAL300025497411
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497411'
/scratch/stefan/7787277/working/building/REAL300025497411 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497411

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497411/0 /scratch/stefan/7787277/working/building/REAL300025497411 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 267)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/267
`/scratch/stefan/7787277/working/3D/267' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=NNC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497411.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497411.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497411/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497411 none O=C(CC1=NNC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 21, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 26, 92, 92, 92, 92, 92, 1, 21, 21, 23, 23, 23, 5, 1, 1, 1, 1, 1, 14, 14, 92, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 230
number of broken/clashed sets: 55
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497411 none O=C(CC1=NNC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 201, 201, 201, 201, 201, 92, 92, 92, 92, 92, 59, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 92, 201, 201, 201, 201, 201, 125, 92, 92, 92, 92, 92, 29, 29, 1, 92, 92] 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])
total number of confs: 793
number of broken/clashed sets: 55
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497411 none O=C(CC1=NNC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 8, 8, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 11, 11, 23, 23, 23, 23, 23, 42, 42, 76, 122, 201, 201, 201, 201, 201, 23, 5, 5, 1, 1, 1, 11, 23, 23, 23, 23, 23, 76, 76, 201, 23, 23] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 514
number of broken/clashed sets: 55
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497411 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497411
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497411/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497411
Building REAL300025497412
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497412'
/scratch/stefan/7787277/working/building/REAL300025497412 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497412

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497412/0 /scratch/stefan/7787277/working/building/REAL300025497412 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 268)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/268
`/scratch/stefan/7787277/working/3D/268' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NC=C2F)C1)

`REAL300025497412.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497412.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497412/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497412 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NC=C2F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 15, 5, 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, 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, 37, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 6, 12, 12, 12, 1, 18, 18, 114, 1, 1, 1, 1, 1, 4, 12, 12, 12, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37])
total number of confs: 234
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497412 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NC=C2F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 15, 5, 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, 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: [35, 12, 35, 74, 120, 201, 201, 201, 201, 201, 12, 12, 12, 12, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 12, 74, 74, 201, 12, 12, 12, 12, 12, 8, 1, 1, 1, 12, 12] 201
rigid atoms, others: [35, 36, 37, 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, 38, 39])
total number of confs: 493
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497412 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NC=C2F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 15, 5, 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, 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, 41, 13, 1, 1, 1, 1, 1, 1, 1, 82, 114, 114, 114, 114, 114, 173, 173, 173, 201, 201, 201, 201, 201, 201, 114, 41, 41, 1, 114, 114, 114, 114, 114, 173, 201, 201, 201, 114, 114] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 592
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497412 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497412
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497412/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497412
Building REAL300025497413
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497413'
/scratch/stefan/7787277/working/building/REAL300025497413 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497413

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497413/0 /scratch/stefan/7787277/working/building/REAL300025497413 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 269)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/269
`/scratch/stefan/7787277/working/3D/269' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=NN1C)

`REAL300025497413.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497413.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497413/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497413 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 8, 5, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 46, 122, 122, 122, 122, 122, 1, 17, 18, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 26, 26, 122, 1, 1, 18, 18, 18] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 21, 39, 38, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42])
total number of confs: 265
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497413 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 8, 5, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 162, 162, 162, 122, 122, 122, 122, 122, 94, 40, 94, 13, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 201, 201, 201, 162, 122, 122, 122, 122, 122, 40, 40, 1, 122, 122, 201, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 561
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497413 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 8, 5, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 18, 18, 18, 18, 18, 42, 42, 103, 133, 201, 201, 201, 201, 201, 18, 1, 1, 1, 1, 2, 2, 2, 9, 18, 18, 18, 18, 18, 103, 103, 201, 18, 18, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 22, 23, 24, 25] set([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: 598
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497413 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497413
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497413/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497413
Building REAL300025497414
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497414'
/scratch/stefan/7787277/working/building/REAL300025497414 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497414

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497414/0 /scratch/stefan/7787277/working/building/REAL300025497414 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 270)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/270
`/scratch/stefan/7787277/working/3D/270' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497414.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497414.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497414/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497414 none CC1=CC=NC=C1C(=O)NC1C=CCN(C(=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.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 31, 67, 67, 67, 67, 67, 1, 23, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 1, 17, 17, 67, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 177
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497414 none CC1=CC=NC=C1C(=O)NC1C=CCN(C(=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.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 84, 84, 84, 67, 67, 67, 67, 67, 52, 34, 52, 13, 1, 1, 1, 1, 1, 1, 1, 67, 201, 201, 201, 201, 201, 201, 84, 67, 67, 67, 67, 67, 34, 34, 1, 67, 67] 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])
total number of confs: 448
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497414 none CC1=CC=NC=C1C(=O)NC1C=CCN(C(=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.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 23, 23, 23, 23, 23, 48, 48, 90, 134, 201, 201, 201, 201, 201, 23, 2, 2, 2, 1, 1, 1, 9, 23, 23, 23, 23, 23, 90, 90, 201, 23, 23] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 544
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497414 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497414
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497414/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497414
Building REAL300025497415
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497415'
/scratch/stefan/7787277/working/building/REAL300025497415 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497415

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497415/0 /scratch/stefan/7787277/working/building/REAL300025497415 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 271)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/271
`/scratch/stefan/7787277/working/3D/271' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497415.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497415.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497415/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497415 none CC1=CN=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 6, 6, 17, 41, 120, 120, 120, 120, 120, 1, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 17, 17, 120, 1, 1, 14] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42])
total number of confs: 231
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497415 none CC1=CN=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 139, 139, 139, 120, 120, 120, 120, 120, 103, 51, 103, 13, 1, 1, 1, 1, 1, 1, 1, 120, 201, 201, 201, 201, 201, 201, 139, 120, 120, 120, 120, 120, 51, 51, 1, 120, 120, 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])
total number of confs: 538
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497415 none CC1=CN=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 33, 33, 64, 114, 201, 201, 201, 201, 201, 14, 1, 2, 2, 2, 1, 1, 5, 14, 14, 14, 14, 14, 64, 64, 201, 14, 14, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 42, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 463
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497415 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497415
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497415/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497415
Building REAL300025497416
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497416'
/scratch/stefan/7787277/working/building/REAL300025497416 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025497416

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497416/0 /scratch/stefan/7787277/working/building/REAL300025497416 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 272)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/272
`/scratch/stefan/7787277/working/3D/272' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497416.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497416.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497416/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497416 none CN1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 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: [22, 22, 22, 22, 22, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 41, 108, 108, 108, 108, 108, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 1, 1, 1, 1, 1, 24, 24, 108, 1, 1, 22, 22] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46])
total number of confs: 263
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497416 none CN1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 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, 156, 156, 156, 108, 108, 108, 108, 108, 82, 37, 82, 13, 1, 1, 1, 1, 1, 1, 1, 108, 201, 201, 201, 201, 201, 201, 201, 201, 201, 156, 108, 108, 108, 108, 108, 37, 37, 1, 108, 108, 201, 201] 201
rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 637
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497416 none CN1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 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, 10, 10, 10, 22, 22, 22, 22, 22, 55, 55, 114, 144, 201, 201, 201, 201, 201, 22, 1, 2, 2, 2, 1, 1, 1, 1, 1, 10, 22, 22, 22, 22, 22, 114, 114, 201, 22, 22, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 45, 46, 25, 33, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 606
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497416 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497416/1 /scratch/stefan/7787277/working/building/REAL300025497416 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 273)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/273
`/scratch/stefan/7787277/working/3D/273' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497416.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497416.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497416/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497416 none C[N@@H+]1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
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: [4, 4, 4, 4, 4, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 5, 5, 5, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 5, 5, 5, 1, 1, 4, 4] 5
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47])
total number of confs: 30
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497416 none C[N@@H+]1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 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, 1, 5, 5, 5, 5] 5
rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 6
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497416 none C[N@@H+]1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 5, 5, 4, 4, 1, 1] 5
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 46, 47, 33, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 15
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497416 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `2'
/scratch/stefan/7787277/working/building/REAL300025497416/2 /scratch/stefan/7787277/working/building/REAL300025497416 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 2 (index: 274)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/274
`/scratch/stefan/7787277/working/3D/274' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497416.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025497416.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497416/2/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: REAL300025497416 none C[N@H+]1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 13, 18, 32, 32, 32, 32, 32, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 13, 13, 32, 1, 1, 13, 13] 50
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47])
total number of confs: 109
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497416 none C[N@H+]1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [50, 50, 50, 50, 50, 50, 48, 48, 48, 32, 32, 32, 32, 32, 30, 23, 30, 12, 1, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 32, 32, 32, 32, 32, 23, 23, 1, 32, 32, 50, 50] 50
rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 159
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497416 none C[N@H+]1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 23, 23, 32, 39, 50, 50, 50, 50, 50, 13, 1, 2, 2, 2, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 32, 32, 50, 13, 13, 1, 1] 50
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 46, 47, 33, 26, 30, 31] set([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])
total number of confs: 152
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497416 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497416
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497416/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497416/1.*
2: /scratch/stefan/7787277/working/building/REAL300025497416/2.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497416
Building REAL300025497417
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497417'
/scratch/stefan/7787277/working/building/REAL300025497417 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497417

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497417/0 /scratch/stefan/7787277/working/building/REAL300025497417 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 275)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/275
`/scratch/stefan/7787277/working/3D/275' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1)

`REAL300025497417.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497417.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497417/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497417 none CC1=NC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 41, 115, 115, 115, 115, 115, 1, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 24, 24, 115, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 248
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497417 none CC1=NC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 174, 174, 174, 115, 115, 115, 115, 115, 87, 42, 87, 13, 1, 1, 1, 1, 1, 1, 1, 115, 201, 201, 201, 201, 201, 201, 201, 174, 115, 115, 115, 115, 115, 42, 42, 1, 115, 115] 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])
total number of confs: 606
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497417 none CC1=NC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 5, 17, 17, 17, 17, 17, 42, 42, 98, 133, 201, 201, 201, 201, 201, 17, 1, 2, 2, 2, 2, 2, 2, 6, 17, 17, 17, 17, 17, 98, 98, 201, 17, 17] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 586
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497417 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497417
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497417/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497417
Building REAL300025497418
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497418'
/scratch/stefan/7787277/working/building/REAL300025497418 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497418

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497418/0 /scratch/stefan/7787277/working/building/REAL300025497418 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 276)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/276
`/scratch/stefan/7787277/working/3D/276' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC(F)(F)F)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497418.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497418.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497418/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497418 none O=C(CCC(F)(F)F)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 15, 15, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 178, 201, 201, 201, 201, 54, 54, 54, 54, 54, 43, 34, 43, 13, 1, 1, 1, 1, 1, 1, 1, 54, 178, 178, 201, 201, 73, 54, 54, 54, 54, 54, 34, 34, 1, 54, 54] 201
rigid atoms, others: [37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 814
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: REAL300025497418 none O=C(CCC(F)(F)F)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'F', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 15, 15, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 24, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 54, 54, 54, 54, 54, 1, 21, 21, 25, 25, 4, 1, 1, 1, 1, 1, 10, 10, 54, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 39, 8, 9, 10, 11, 12, 13, 14, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 200
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497418 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497418
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497418/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497418
Building REAL300025497419
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497419'
/scratch/stefan/7787277/working/building/REAL300025497419 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497419

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497419/0 /scratch/stefan/7787277/working/building/REAL300025497419 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 277)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/277
`/scratch/stefan/7787277/working/3D/277' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCOCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497419.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497419.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497419/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497419 none C=CCOCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
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, 131, 131, 120, 43, 43, 43, 42, 42, 42, 42, 42, 42, 30, 42, 13, 1, 1, 1, 1, 1, 1, 1, 42, 201, 201, 201, 201, 201, 131, 131, 131, 131, 120, 120, 43, 42, 42, 42, 42, 42, 30, 30, 1, 42, 42] 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])
total number of confs: 815
number of broken/clashed sets: 172
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497419 none C=CCOCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 37, 20, 13, 13, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 42, 42, 42, 42, 42, 1, 47, 47, 47, 37, 37, 13, 13, 13, 13, 9, 9, 3, 1, 1, 1, 1, 1, 6, 6, 42, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 236
number of broken/clashed sets: 172
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497419 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497419
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497419/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497419
Building REAL300025497420
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497420'
/scratch/stefan/7787277/working/building/REAL300025497420 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497420

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497420/0 /scratch/stefan/7787277/working/building/REAL300025497420 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 278)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/278
`/scratch/stefan/7787277/working/3D/278' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497420.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497420.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497420/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497420 none O=C(CC1CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 20, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 12, 51, 51, 51, 51, 51, 1, 20, 20, 37, 37, 37, 37, 37, 37, 37, 5, 1, 1, 1, 1, 1, 7, 6, 51, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 208
number of broken/clashed sets: 73
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497420 none O=C(CC1CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [80, 80, 80, 136, 201, 201, 201, 51, 51, 51, 51, 51, 44, 27, 44, 13, 1, 1, 1, 1, 1, 1, 1, 51, 136, 136, 201, 201, 201, 201, 201, 201, 201, 80, 51, 51, 51, 51, 51, 27, 27, 1, 51, 51] 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])
total number of confs: 820
number of broken/clashed sets: 73
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497420 none O=C(CC1CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 1, 1, 1, 1, 1, 19, 19, 37, 37, 37, 37, 37, 46, 46, 95, 140, 201, 201, 201, 201, 201, 37, 4, 4, 1, 1, 1, 1, 1, 1, 1, 19, 37, 37, 37, 37, 37, 95, 95, 201, 37, 37] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 26, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 566
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497420 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497420
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497420/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497420
Building REAL300025497421
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497421'
/scratch/stefan/7787277/working/building/REAL300025497421 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497421

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497421/0 /scratch/stefan/7787277/working/building/REAL300025497421 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 279)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/279
`/scratch/stefan/7787277/working/3D/279' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC(=O)N2)C1)

`REAL300025497421.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497421.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497421/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497421 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 21, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 18, 1, 13, 13, 74, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 33, 40, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38])
total number of confs: 158
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497421 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 18, 39, 76, 110, 201, 201, 201, 201, 201, 18, 18, 18, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 18, 76, 76, 201, 18, 18, 18, 18, 18, 7, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [35, 36, 37, 38, 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, 39, 40])
total number of confs: 506
number of broken/clashed sets: 24
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497421 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 37, 13, 1, 1, 1, 1, 1, 1, 1, 56, 74, 74, 74, 74, 74, 103, 103, 103, 201, 201, 201, 201, 201, 201, 74, 37, 37, 1, 74, 74, 74, 74, 74, 103, 201, 201, 201, 201, 74, 74] 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: 477
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497421 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497421
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497421/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497421
Building REAL300025497422
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497422'
/scratch/stefan/7787277/working/building/REAL300025497422 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497422

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497422/0 /scratch/stefan/7787277/working/building/REAL300025497422 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 280)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/280
`/scratch/stefan/7787277/working/3D/280' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1(C)C)

`REAL300025497422.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497422.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497422/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497422 none CC1(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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: [10, 10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 39, 123, 123, 123, 123, 123, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 1, 20, 20, 123, 1, 1, 10, 10, 10, 10, 10, 10] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49])
total number of confs: 244
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497422 none CC1(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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: [201, 201, 201, 155, 155, 155, 123, 123, 123, 123, 123, 95, 47, 95, 13, 1, 1, 1, 1, 1, 1, 1, 123, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 155, 123, 123, 123, 123, 123, 47, 47, 1, 123, 123, 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])
total number of confs: 663
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497422 none CC1(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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: [1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 32, 32, 66, 109, 201, 201, 201, 201, 201, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 4, 10, 10, 10, 10, 10, 66, 66, 201, 10, 10, 1, 1, 1, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 32, 44, 45, 46, 23, 24, 25, 26, 27, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 47, 48, 49])
total number of confs: 472
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497422 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497422
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497422/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497422
Building REAL300025497423
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497423'
/scratch/stefan/7787277/working/building/REAL300025497423 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497423

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497423/0 /scratch/stefan/7787277/working/building/REAL300025497423 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 281)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/281
`/scratch/stefan/7787277/working/3D/281' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)OC=N1)

`REAL300025497423.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497423.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497423/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497423 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)OC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 8, 7, 7, 7, 6, 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, 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 37, 138, 138, 138, 138, 138, 1, 12, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 14, 14, 138, 1, 1, 12] 201
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 37, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39])
total number of confs: 233
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497423 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)OC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 8, 7, 7, 7, 6, 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, 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, 185, 185, 185, 138, 138, 138, 138, 138, 108, 46, 108, 13, 1, 1, 1, 1, 1, 1, 1, 138, 201, 201, 201, 201, 201, 201, 185, 138, 138, 138, 138, 138, 46, 46, 1, 138, 138, 201] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39])
total number of confs: 587
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497423 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)OC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 8, 7, 7, 7, 6, 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, 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, 12, 12, 12, 12, 12, 31, 31, 77, 130, 201, 201, 201, 201, 201, 12, 1, 1, 1, 2, 2, 2, 4, 12, 12, 12, 12, 12, 77, 77, 201, 12, 12, 1] 201
rigid atoms, others: [0, 1, 2, 3, 39, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 518
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497423 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497423
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497423/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497423
Building REAL300025497424
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497424'
/scratch/stefan/7787277/working/building/REAL300025497424 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497424

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497424/0 /scratch/stefan/7787277/working/building/REAL300025497424 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 282)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/282
`/scratch/stefan/7787277/working/3D/282' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1)

`REAL300025497424.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497424.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497424/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497424 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [34, 24, 24, 24, 18, 18, 18, 18, 18, 18, 18, 18, 12, 1, 1, 1, 1, 1, 1, 1, 18, 34, 34, 34, 34, 34, 34, 34, 24, 18, 18, 18, 18, 18, 18, 18, 1, 18, 18, 34, 34, 34, 34, 34] 34
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: 113
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497424 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 9, 9, 9, 21, 21, 21, 21, 21, 29, 29, 30, 30, 34, 34, 34, 34, 34, 21, 1, 1, 1, 3, 3, 3, 3, 9, 21, 21, 21, 21, 21, 30, 30, 34, 21, 21, 1, 1, 1, 1, 1] 34
rigid atoms, others: [1, 39, 40, 41, 42, 43, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 106
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497424 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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
34  conformations in input
total number of sets (complete confs): 34
using default count positions algorithm for smaller data
unique positions, atoms: [21, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 8, 18, 18, 18, 18, 18, 1, 21, 21, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 7, 7, 18, 1, 1, 21, 21, 21, 21, 21] 34
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 37, 20, 38, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40, 41, 42, 43])
total number of confs: 108
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497424 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497424
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497424/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497424
Building REAL300025497425
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497425'
/scratch/stefan/7787277/working/building/REAL300025497425 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497425

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497425/0 /scratch/stefan/7787277/working/building/REAL300025497425 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 283)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/283
`/scratch/stefan/7787277/working/3D/283' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2C3CCCC32)C1)

`REAL300025497425.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497425.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497425/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497425 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2C3CCCC32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens need 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, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 4, 4, 4, 27, 27, 27, 27, 27, 1, 10, 10, 62, 1, 1, 1, 1, 1, 4, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1] 201
rigid atoms, others: [32, 1, 43, 44, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 170
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497425 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2C3CCCC32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 27, 49, 76, 105, 201, 201, 201, 201, 201, 27, 27, 27, 27, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 27, 76, 76, 201, 27, 27, 27, 27, 27, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 201
rigid atoms, others: [34, 35, 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, 43, 44])
total number of confs: 506
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497425 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2C3CCCC32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 30, 13, 1, 1, 1, 1, 1, 1, 1, 48, 62, 62, 62, 62, 62, 94, 94, 94, 201, 201, 201, 201, 201, 62, 30, 30, 1, 62, 62, 62, 62, 62, 94, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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: 639
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497425 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497425
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497425/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497425
Building REAL300025497426
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497426'
/scratch/stefan/7787277/working/building/REAL300025497426 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497426

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497426/0 /scratch/stefan/7787277/working/building/REAL300025497426 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 284)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/284
`/scratch/stefan/7787277/working/3D/284' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: N#CC1=CNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497426.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497426.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497426/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497426 none N#CC1=CNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [15, 15, 15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 30, 69, 69, 69, 69, 69, 1, 15, 15, 15, 5, 1, 1, 1, 1, 1, 19, 19, 69, 1, 1, 15] 97
rigid atoms, others: [32, 33, 37, 38, 8, 9, 10, 11, 12, 13, 14, 24, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 34, 35, 36, 39])
total number of confs: 172
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497426 none N#CC1=CNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [97, 97, 97, 97, 97, 79, 79, 79, 69, 69, 69, 69, 69, 62, 30, 62, 13, 1, 1, 1, 1, 1, 1, 1, 69, 97, 97, 97, 79, 69, 69, 69, 69, 69, 30, 30, 1, 69, 69, 97] 97
rigid atoms, others: [36, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39])
total number of confs: 282
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497426 none N#CC1=CNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
97  conformations in input
total number of sets (complete confs): 97
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 15, 31, 31, 53, 68, 97, 97, 97, 97, 97, 15, 1, 1, 1, 7, 15, 15, 15, 15, 15, 53, 53, 97, 15, 15, 1] 97
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 276
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497426 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497426
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497426/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497426
Building REAL300025497427
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497427'
/scratch/stefan/7787277/working/building/REAL300025497427 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497427

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497427/0 /scratch/stefan/7787277/working/building/REAL300025497427 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 285)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/285
`/scratch/stefan/7787277/working/3D/285' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CSC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497427.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497427.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497427/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497427 none CC1=CSC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 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, 6, 7, 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: [17, 17, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 25, 102, 102, 102, 102, 102, 1, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 11, 11, 102, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 188
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497427 none CC1=CSC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 124, 124, 124, 102, 102, 102, 102, 102, 85, 46, 85, 13, 1, 1, 1, 1, 1, 1, 1, 102, 201, 201, 201, 201, 201, 124, 102, 102, 102, 102, 102, 46, 46, 1, 102, 102] 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])
total number of confs: 529
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497427 none CC1=CSC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 14, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 17, 17, 17, 32, 32, 65, 108, 201, 201, 201, 201, 201, 17, 2, 2, 2, 1, 1, 8, 17, 17, 17, 17, 17, 65, 65, 201, 17, 17] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 501
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497427 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497427
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497427/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497427
Building REAL300025497428
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497428'
/scratch/stefan/7787277/working/building/REAL300025497428 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497428

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497428/0 /scratch/stefan/7787277/working/building/REAL300025497428 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 286)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/286
`/scratch/stefan/7787277/working/3D/286' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497428.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497428.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497428/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497428 none O=C(CCC1CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need 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, 17, 20, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 11, 38, 38, 38, 38, 38, 1, 17, 17, 22, 22, 39, 39, 39, 39, 39, 39, 39, 3, 1, 1, 1, 1, 1, 5, 5, 38, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 211
number of broken/clashed sets: 69
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497428 none O=C(CCC1CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 143, 120, 201, 201, 201, 38, 38, 38, 38, 38, 34, 25, 34, 13, 1, 1, 1, 1, 1, 1, 1, 38, 143, 143, 145, 145, 201, 201, 201, 201, 201, 201, 201, 40, 38, 38, 38, 38, 38, 25, 25, 1, 38, 38] 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])
total number of confs: 888
number of broken/clashed sets: 69
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497428 none O=C(CCC1CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 5, 1, 1, 1, 1, 1, 28, 28, 39, 39, 39, 39, 39, 44, 44, 90, 140, 201, 201, 201, 201, 201, 39, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 28, 39, 39, 39, 39, 39, 90, 90, 201, 39, 39] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 35, 29, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 574
number of broken/clashed sets: 69
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497428 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497428
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497428/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497428
Building REAL300025497429
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497429'
/scratch/stefan/7787277/working/building/REAL300025497429 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497429

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497429/0 /scratch/stefan/7787277/working/building/REAL300025497429 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 287)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/287
`/scratch/stefan/7787277/working/3D/287' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1)

`REAL300025497429.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497429.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497429/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497429 none CC1=CC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens 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, 6, 6, 22, 38, 111, 111, 111, 111, 111, 1, 14, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 22, 22, 111, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 234
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497429 none CC1=CC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 147, 147, 147, 111, 111, 111, 111, 111, 85, 41, 85, 13, 1, 1, 1, 1, 1, 1, 1, 111, 201, 201, 201, 201, 201, 201, 201, 201, 147, 111, 111, 111, 111, 111, 41, 41, 1, 111, 111] 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])
total number of confs: 574
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497429 none CC1=CC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 14, 14, 14, 14, 14, 43, 43, 93, 132, 201, 201, 201, 201, 201, 14, 1, 2, 2, 2, 1, 2, 2, 2, 4, 14, 14, 14, 14, 14, 93, 93, 201, 14, 14] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 564
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497429 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497429
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497429/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497429
Building REAL300025497430
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497430'
/scratch/stefan/7787277/working/building/REAL300025497430 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497430

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497430/0 /scratch/stefan/7787277/working/building/REAL300025497430 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 288)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/288
`/scratch/stefan/7787277/working/3D/288' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=NN=CN1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497430.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497430.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497430/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497430 none O=C(CCC1=NN=CN1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [5, 5, 5, 10, 10, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 16, 53, 53, 53, 53, 53, 1, 10, 10, 10, 10, 11, 11, 5, 1, 1, 1, 1, 1, 11, 11, 53, 1, 1] 66
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 135
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497430 none O=C(CCC1=NN=CN1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [62, 62, 62, 66, 66, 66, 66, 66, 66, 53, 53, 53, 53, 53, 41, 27, 41, 13, 1, 1, 1, 1, 1, 1, 1, 53, 66, 66, 66, 66, 66, 66, 62, 53, 53, 53, 53, 53, 27, 27, 1, 53, 53] 66
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])
total number of confs: 221
number of broken/clashed sets: 34
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497430 none O=C(CCC1=NN=CN1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [6, 4, 4, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 20, 20, 26, 38, 66, 66, 66, 66, 66, 11, 4, 4, 4, 4, 1, 1, 6, 11, 11, 11, 11, 11, 26, 26, 66, 11, 11] 66
rigid atoms, others: [3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 170
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497430 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497430/1 /scratch/stefan/7787277/working/building/REAL300025497430 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 289)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/289
`/scratch/stefan/7787277/working/3D/289' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=NNC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497430.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497430.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497430/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497430 none O=C(CCC1=NNC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 6, 6, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 13, 13, 13, 13, 13, 1, 6, 6, 6, 6, 10, 10, 3, 1, 1, 1, 1, 1, 4, 4, 13, 1, 1] 19
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 52
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497430 none O=C(CCC1=NNC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [14, 14, 14, 17, 17, 19, 19, 19, 19, 13, 13, 13, 13, 13, 12, 12, 12, 10, 1, 1, 1, 1, 1, 1, 1, 13, 17, 17, 17, 17, 19, 19, 14, 13, 13, 13, 13, 13, 12, 12, 1, 13, 13] 19
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])
total number of confs: 51
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497430 none O=C(CCC1=NNC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 8, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [9, 8, 7, 1, 1, 1, 1, 1, 1, 9, 9, 10, 10, 10, 10, 10, 10, 10, 11, 13, 19, 19, 19, 19, 19, 10, 8, 8, 7, 7, 1, 1, 9, 10, 10, 10, 10, 10, 11, 11, 19, 10, 10] 19
rigid atoms, others: [3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 56
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497430 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497430
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497430/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497430/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497430
Building REAL300025497431
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497431'
/scratch/stefan/7787277/working/building/REAL300025497431 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497431

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497431/0 /scratch/stefan/7787277/working/building/REAL300025497431 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 290)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/290
`/scratch/stefan/7787277/working/3D/290' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497431.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497431.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497431/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497431 none CC1=CC=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 44, 114, 114, 114, 114, 114, 1, 16, 16, 16, 16, 16, 16, 4, 1, 1, 1, 1, 1, 24, 24, 114, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 251
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497431 none CC1=CC=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 159, 159, 159, 114, 114, 114, 114, 114, 83, 37, 83, 13, 1, 1, 1, 1, 1, 1, 1, 114, 201, 201, 201, 201, 201, 201, 159, 114, 114, 114, 114, 114, 37, 37, 1, 114, 114] 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])
total number of confs: 570
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497431 none CC1=CC=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 16, 16, 16, 16, 16, 41, 41, 100, 138, 201, 201, 201, 201, 201, 16, 2, 2, 2, 1, 1, 1, 7, 16, 16, 16, 16, 16, 100, 100, 201, 16, 16] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 575
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497431 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497431
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497431/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497431
Building REAL300025497432
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497432'
/scratch/stefan/7787277/working/building/REAL300025497432 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497432

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497432/0 /scratch/stefan/7787277/working/building/REAL300025497432 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 291)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/291
`/scratch/stefan/7787277/working/3D/291' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC=C(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497432.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497432.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497432/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497432 none CC=C(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 136, 201, 136, 136, 109, 109, 109, 109, 109, 92, 36, 92, 13, 1, 1, 1, 1, 1, 1, 1, 109, 201, 201, 201, 201, 201, 201, 201, 136, 109, 109, 109, 109, 109, 36, 36, 1, 109, 109] 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])
total number of confs: 638
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: REAL300025497432 none CC=C(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 30, 109, 109, 109, 109, 109, 1, 19, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 14, 14, 109, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 225
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497432 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497432
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497432/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497432
Building REAL300025497433
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497433'
/scratch/stefan/7787277/working/building/REAL300025497433 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497433

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497433/0 /scratch/stefan/7787277/working/building/REAL300025497433 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 292)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/292
`/scratch/stefan/7787277/working/3D/292' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1CCOC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497433.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497433.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497433/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497433 none O=C(CCC1CCOC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 22, 28, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 38, 38, 38, 38, 38, 1, 22, 22, 31, 31, 41, 41, 41, 41, 41, 41, 41, 4, 1, 1, 1, 1, 1, 5, 5, 38, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 233
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497433 none O=C(CCC1CCOC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 170, 170, 201, 201, 201, 201, 38, 38, 38, 38, 38, 36, 27, 36, 12, 1, 1, 1, 1, 1, 1, 1, 38, 170, 170, 188, 188, 201, 201, 201, 201, 201, 201, 201, 64, 38, 38, 38, 38, 38, 27, 27, 1, 38, 38] 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])
total number of confs: 855
number of broken/clashed sets: 50
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497433 none O=C(CCC1CCOC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 26, 26, 41, 41, 41, 41, 41, 44, 44, 91, 138, 201, 201, 201, 201, 201, 41, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 26, 41, 41, 41, 41, 41, 91, 91, 201, 41, 41] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 35, 36, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 567
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497433 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497433
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497433/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497433
Building REAL300025497434
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497434'
/scratch/stefan/7787277/working/building/REAL300025497434 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497434

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497434/0 /scratch/stefan/7787277/working/building/REAL300025497434 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 293)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/293
`/scratch/stefan/7787277/working/3D/293' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=COC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497434.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497434.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497434/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497434 none O=C(CCC1=COC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 12, 1, 1, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 20, 24, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 11, 45, 45, 45, 45, 45, 1, 20, 20, 24, 24, 42, 42, 42, 5, 1, 1, 1, 1, 1, 6, 6, 45, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 195
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497434 none O=C(CCC1=COC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 12, 1, 1, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 114, 124, 201, 201, 201, 201, 45, 45, 45, 45, 45, 38, 27, 38, 13, 1, 1, 1, 1, 1, 1, 1, 45, 114, 114, 124, 124, 201, 201, 201, 63, 45, 45, 45, 45, 45, 27, 27, 1, 45, 45] 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])
total number of confs: 636
number of broken/clashed sets: 53
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497434 none O=C(CCC1=COC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 12, 1, 1, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 2, 1, 1, 1, 1, 1, 1, 24, 24, 42, 42, 42, 42, 42, 48, 48, 94, 135, 201, 201, 201, 201, 201, 42, 6, 6, 2, 2, 1, 1, 1, 24, 42, 42, 42, 42, 42, 94, 94, 201, 42, 42] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 577
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497434 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497434
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497434/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497434
Building REAL300025497435
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497435'
/scratch/stefan/7787277/working/building/REAL300025497435 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497435

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497435/0 /scratch/stefan/7787277/working/building/REAL300025497435 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 294)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/294
`/scratch/stefan/7787277/working/3D/294' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC(F)(F)C2)C1)

`REAL300025497435.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497435.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497435/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497435 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC(F)(F)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 22, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 19, 19, 1, 13, 13, 72, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [32, 1, 39, 40, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38])
total number of confs: 174
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497435 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC(F)(F)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 19, 45, 84, 112, 201, 201, 201, 201, 201, 19, 19, 19, 19, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 19, 84, 84, 201, 19, 19, 19, 19, 19, 10, 1, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [34, 35, 36, 37, 38, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40])
total number of confs: 534
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497435 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC(F)(F)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [50, 30, 12, 1, 1, 1, 1, 1, 1, 1, 50, 72, 72, 72, 72, 72, 103, 103, 103, 201, 201, 201, 201, 201, 72, 30, 30, 1, 72, 72, 72, 72, 72, 103, 201, 201, 201, 201, 201, 72, 72] 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: 636
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497435 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497435
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497435/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497435
Building REAL300025497436
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497436'
/scratch/stefan/7787277/working/building/REAL300025497436 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497436

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497436/0 /scratch/stefan/7787277/working/building/REAL300025497436 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 295)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/295
`/scratch/stefan/7787277/working/3D/295' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497436.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497436.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497436/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497436 none CC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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
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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 31, 69, 69, 69, 69, 69, 1, 25, 25, 25, 25, 25, 25, 25, 25, 5, 1, 1, 1, 1, 1, 18, 18, 69, 1, 1, 25, 25] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43])
total number of confs: 209
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497436 none CC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 84, 84, 84, 69, 69, 69, 69, 69, 59, 37, 59, 13, 1, 1, 1, 1, 1, 1, 1, 69, 201, 201, 201, 201, 201, 201, 201, 201, 84, 69, 69, 69, 69, 69, 37, 37, 1, 69, 69, 201, 201] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 639
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497436 none CC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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
201  conformations in 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, 25, 25, 25, 25, 25, 54, 54, 95, 134, 201, 201, 201, 201, 201, 25, 1, 2, 2, 2, 1, 1, 1, 1, 9, 25, 25, 25, 25, 25, 95, 95, 201, 25, 25, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 42, 43, 23, 27, 28, 29, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 557
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497436 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497436
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497436/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497436
Building REAL300025497437
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497437'
/scratch/stefan/7787277/working/building/REAL300025497437 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497437

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497437/0 /scratch/stefan/7787277/working/building/REAL300025497437 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 296)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/296
`/scratch/stefan/7787277/working/3D/296' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CCCC1)

`REAL300025497437.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497437.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497437/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497437 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 5, 5, 5, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 112, 112, 112, 82, 82, 82, 82, 82, 72, 39, 72, 13, 1, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 201, 201, 201, 201, 201, 112, 82, 82, 82, 82, 82, 39, 39, 1, 82, 82, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 659
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497437 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 5, 5, 5, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  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, 25, 25, 25, 25, 25, 58, 58, 114, 145, 201, 201, 201, 201, 201, 25, 1, 1, 1, 1, 1, 2, 2, 2, 9, 25, 25, 25, 25, 25, 114, 114, 201, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 40, 41, 42, 43, 44, 45, 46, 47, 21, 22, 23, 24, 25] set([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])
total number of confs: 590
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497437 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 5, 5, 5, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 30, 82, 82, 82, 82, 82, 1, 25, 25, 25, 25, 25, 25, 25, 25, 5, 1, 1, 1, 1, 1, 19, 19, 82, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 39, 20, 38, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 218
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497437 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497437
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497437/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497437
Building REAL300025497438
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497438'
/scratch/stefan/7787277/working/building/REAL300025497438 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497438

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497438/0 /scratch/stefan/7787277/working/building/REAL300025497438 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 297)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/297
`/scratch/stefan/7787277/working/3D/297' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497438.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497438.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497438/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497438 none O=C(CC1CCCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 25, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 24, 87, 87, 87, 87, 87, 1, 25, 25, 31, 31, 31, 31, 31, 31, 31, 31, 31, 5, 1, 1, 1, 1, 1, 13, 13, 87, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 255
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497438 none O=C(CC1CCCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [118, 118, 118, 201, 201, 201, 201, 201, 201, 87, 87, 87, 87, 87, 58, 30, 58, 13, 1, 1, 1, 1, 1, 1, 1, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 118, 87, 87, 87, 87, 87, 30, 30, 1, 87, 87] 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])
total number of confs: 712
number of broken/clashed sets: 54
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497438 none O=C(CC1CCCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 1, 1, 17, 17, 31, 31, 31, 31, 31, 47, 47, 77, 121, 201, 201, 201, 201, 201, 31, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 31, 31, 31, 31, 31, 77, 77, 201, 31, 31] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 513
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497438 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497438
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497438/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497438
Building REAL300025497439
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497439'
/scratch/stefan/7787277/working/building/REAL300025497439 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497439

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497439/0 /scratch/stefan/7787277/working/building/REAL300025497439 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 298)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/298
`/scratch/stefan/7787277/working/3D/298' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1)

`REAL300025497439.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497439.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497439/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497439 none CC1=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.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, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [24, 24, 24, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 23, 84, 84, 84, 84, 84, 1, 24, 24, 24, 24, 24, 24, 20, 20, 5, 1, 1, 1, 1, 1, 13, 13, 84, 1, 1, 24] 201
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 216
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497439 none CC1=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.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, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 113, 113, 113, 84, 84, 84, 84, 84, 53, 30, 53, 13, 1, 1, 1, 1, 1, 1, 1, 84, 201, 201, 201, 201, 201, 201, 201, 201, 113, 84, 84, 84, 84, 84, 30, 30, 1, 84, 84, 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])
total number of confs: 789
number of broken/clashed sets: 50
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497439 none CC1=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.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, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 5, 13, 13, 13, 24, 24, 24, 24, 24, 44, 44, 75, 114, 201, 201, 201, 201, 201, 24, 1, 1, 2, 2, 2, 1, 5, 5, 13, 24, 24, 24, 24, 24, 75, 75, 201, 24, 24, 1] 201
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: 522
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497439 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497439/1 /scratch/stefan/7787277/working/building/REAL300025497439 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 299)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/299
`/scratch/stefan/7787277/working/3D/299' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497439.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497439.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497439/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497439 none CC1=NNC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 7, 7, 6, 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: [31, 31, 31, 31, 24, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 25, 89, 89, 89, 89, 89, 1, 31, 31, 31, 31, 31, 24, 24, 5, 1, 1, 1, 1, 1, 13, 13, 89, 1, 1, 31] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 245
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497439 none CC1=NNC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 7, 7, 6, 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, 124, 124, 124, 89, 89, 89, 89, 89, 61, 31, 61, 13, 1, 1, 1, 1, 1, 1, 1, 89, 201, 201, 201, 201, 201, 201, 201, 124, 89, 89, 89, 89, 89, 31, 31, 1, 89, 89, 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])
total number of confs: 740
number of broken/clashed sets: 43
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497439 none CC1=NNC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 7, 7, 6, 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, 6, 19, 19, 19, 31, 31, 31, 31, 31, 43, 43, 81, 121, 201, 201, 201, 201, 201, 31, 1, 2, 2, 2, 1, 6, 6, 19, 31, 31, 31, 31, 31, 81, 81, 201, 31, 31, 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: 531
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497439 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497439
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497439/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497439/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497439
Building REAL300025497440
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497440'
/scratch/stefan/7787277/working/building/REAL300025497440 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497440

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497440/0 /scratch/stefan/7787277/working/building/REAL300025497440 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 300)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/300
`/scratch/stefan/7787277/working/3D/300' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C=C1CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497440.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497440.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497440/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497440 none O=C(C=C1CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 31, 80, 80, 80, 80, 80, 1, 25, 25, 25, 25, 25, 25, 25, 5, 1, 1, 1, 1, 1, 18, 18, 80, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 221
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497440 none O=C(C=C1CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 107, 107, 201, 201, 201, 201, 80, 80, 80, 80, 80, 67, 37, 67, 13, 1, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 201, 201, 201, 201, 107, 80, 80, 80, 80, 80, 37, 37, 1, 80, 80] 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])
total number of confs: 670
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497440 none O=C(C=C1CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 25, 25, 25, 25, 25, 54, 54, 95, 139, 201, 201, 201, 201, 201, 25, 1, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 25, 25, 95, 95, 201, 25, 25] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 24, 25, 26, 27, 28, 29, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 558
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497440 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497440
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497440/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497440
Building REAL300025497441
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497441'
/scratch/stefan/7787277/working/building/REAL300025497441 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497441

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497441/0 /scratch/stefan/7787277/working/building/REAL300025497441 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 301)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/301
`/scratch/stefan/7787277/working/3D/301' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CC(F)=C2)C1)

`REAL300025497441.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497441.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497441/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497441 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CC(F)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 15, 1, 5, 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, 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, 11, 26, 86, 86, 86, 86, 86, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 1, 11, 11, 86, 1, 1, 1, 1, 1, 4, 13, 13, 13, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37])
total number of confs: 164
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497441 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CC(F)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 15, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 13, 28, 66, 104, 201, 201, 201, 201, 201, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 13, 66, 66, 201, 13, 13, 13, 13, 13, 5, 1, 1, 1, 13, 13] 201
rigid atoms, others: [35, 36, 37, 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, 38, 39])
total number of confs: 485
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497441 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CC(F)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 15, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 37, 13, 1, 1, 1, 1, 1, 1, 1, 69, 86, 86, 86, 86, 86, 110, 110, 110, 201, 201, 201, 201, 201, 201, 86, 37, 37, 1, 86, 86, 86, 86, 86, 110, 201, 201, 201, 86, 86] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 499
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497441 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497441
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497441/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497441
Building REAL300025497442
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497442'
/scratch/stefan/7787277/working/building/REAL300025497442 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497442

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497442/0 /scratch/stefan/7787277/working/building/REAL300025497442 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 302)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/302
`/scratch/stefan/7787277/working/3D/302' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)CC)

`REAL300025497442.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497442.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497442/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497442 none CCC(=CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)CC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 1, 11, 8, 5, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [173, 97, 97, 56, 56, 56, 48, 48, 48, 48, 48, 31, 21, 31, 12, 1, 1, 1, 1, 1, 1, 1, 48, 97, 173, 173, 173, 173, 173, 173, 97, 56, 48, 48, 48, 48, 48, 21, 21, 1, 48, 48, 173, 173, 173, 173, 173] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 1229
number of broken/clashed sets: 41
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497442 none CCC(=CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)CC NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 1, 11, 8, 5, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 19, 48, 48, 48, 48, 48, 1, 9, 13, 13, 13, 13, 13, 13, 9, 5, 1, 1, 1, 1, 1, 11, 11, 48, 1, 1, 13, 13, 13, 13, 13] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46])
total number of confs: 166
number of broken/clashed sets: 41
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497442 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497442
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497442/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497442
Building REAL300025497443
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497443'
/scratch/stefan/7787277/working/building/REAL300025497443 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497443

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497443/0 /scratch/stefan/7787277/working/building/REAL300025497443 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 303)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/303
`/scratch/stefan/7787277/working/3D/303' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(=O)NC=C2)C1)

`REAL300025497443.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497443.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497443/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497443 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(=O)NC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 1, 5, 7, 7, 6, 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]
0  hydrogens 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, 14, 23, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 14, 1, 14, 14, 67, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 1, 1] 201
rigid atoms, others: [32, 1, 33, 40, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38])
total number of confs: 151
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497443 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(=O)NC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 1, 5, 7, 7, 6, 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]
0  hydrogens 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, 14, 37, 73, 104, 201, 201, 201, 201, 201, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 73, 73, 201, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 14, 14] 201
rigid atoms, others: [35, 36, 37, 38, 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, 39, 40])
total number of confs: 486
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497443 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(=O)NC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 1, 1, 5, 7, 7, 6, 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]
0  hydrogens 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, 67, 67, 67, 67, 67, 89, 89, 89, 201, 201, 201, 201, 201, 201, 67, 38, 38, 1, 67, 67, 67, 67, 67, 89, 201, 201, 201, 201, 67, 67] 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: 458
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497443 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497443
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497443/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497443
Building REAL300025497444
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497444'
/scratch/stefan/7787277/working/building/REAL300025497444 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497444

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497444/0 /scratch/stefan/7787277/working/building/REAL300025497444 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 304)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/304
`/scratch/stefan/7787277/working/3D/304' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)=C(F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497444.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497444.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497444/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497444 none CC(C)=C(F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 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, 163, 201, 163, 163, 120, 120, 120, 120, 120, 95, 41, 95, 13, 1, 1, 1, 1, 1, 1, 1, 120, 201, 201, 201, 201, 201, 201, 163, 120, 120, 120, 120, 120, 41, 41, 1, 120, 120] 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])
total number of confs: 656
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: REAL300025497444 none CC(C)=C(F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.3', 'C.2', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 5, 1, 15, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 15, 15, 5, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 36, 120, 120, 120, 120, 120, 1, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 17, 17, 120, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 40, 23, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 241
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497444 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497444
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497444/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497444
Building REAL300025497445
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497445'
/scratch/stefan/7787277/working/building/REAL300025497445 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497445

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497445/0 /scratch/stefan/7787277/working/building/REAL300025497445 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 305)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/305
`/scratch/stefan/7787277/working/3D/305' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCNC(=O)C2)C1)

`REAL300025497445.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497445.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497445/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497445 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCNC(=O)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [5, 1, 5, 13, 23, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 18, 1, 13, 13, 78, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 43, 33, 44, 10, 11, 12, 13, 14, 15, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 179
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497445 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCNC(=O)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [40, 18, 40, 82, 111, 201, 201, 201, 201, 201, 18, 18, 18, 18, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 18, 82, 82, 201, 18, 18, 18, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [35, 36, 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, 43, 44])
total number of confs: 521
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497445 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCNC(=O)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [55, 37, 12, 1, 1, 1, 1, 1, 1, 1, 55, 78, 78, 78, 78, 78, 110, 110, 110, 201, 201, 201, 201, 201, 201, 78, 37, 37, 1, 78, 78, 78, 78, 78, 110, 201, 201, 201, 201, 201, 201, 201, 201, 78, 78] 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: 632
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497445 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497445
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497445/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497445
Building REAL300025497446
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497446'
/scratch/stefan/7787277/working/building/REAL300025497446 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497446

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497446/0 /scratch/stefan/7787277/working/building/REAL300025497446 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 306)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/306
`/scratch/stefan/7787277/working/3D/306' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CCCC2)C1)

`REAL300025497446.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497446.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497446/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497446 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 40, 145, 145, 145, 145, 145, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 19, 1, 18, 18, 145, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [1, 40, 41, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 265
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497446 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 19, 52, 93, 125, 201, 201, 201, 201, 201, 19, 19, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 19, 93, 93, 201, 19, 19, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 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, 40, 41])
total number of confs: 507
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497446 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 46, 13, 1, 1, 1, 1, 1, 1, 1, 107, 145, 145, 145, 145, 145, 199, 199, 199, 201, 201, 201, 201, 145, 46, 46, 1, 145, 145, 145, 145, 145, 199, 201, 201, 201, 201, 201, 201, 201, 145, 145] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 627
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497446 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497446
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497446/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497446
Building REAL300025497447
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497447'
/scratch/stefan/7787277/working/building/REAL300025497447 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497447

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497447/0 /scratch/stefan/7787277/working/building/REAL300025497447 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 307)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/307
`/scratch/stefan/7787277/working/3D/307' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C(F)=C2CCCC2)C1)

`REAL300025497447.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497447.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497447/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497447 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C(F)=C2CCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 6, 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, 32, 124, 124, 124, 124, 124, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 18, 1, 15, 15, 124, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 43, 33, 44, 10, 11, 12, 13, 14, 15, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 243
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497447 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C(F)=C2CCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 6, 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: [45, 18, 45, 81, 119, 201, 201, 201, 201, 201, 18, 18, 18, 18, 7, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 18, 81, 81, 201, 18, 18, 18, 18, 18, 8, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [35, 36, 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, 43, 44])
total number of confs: 514
number of broken/clashed sets: 24
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497447 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C(F)=C2CCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'F', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 6, 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: [92, 47, 13, 1, 1, 1, 1, 1, 1, 1, 92, 124, 124, 124, 124, 124, 175, 175, 175, 201, 201, 201, 201, 201, 201, 124, 47, 47, 1, 124, 124, 124, 124, 124, 175, 201, 201, 201, 201, 201, 201, 201, 201, 124, 124] 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: 647
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497447 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497447
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497447/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497447
Building REAL300025497448
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497448'
/scratch/stefan/7787277/working/building/REAL300025497448 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497448

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497448/0 /scratch/stefan/7787277/working/building/REAL300025497448 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 308)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/308
`/scratch/stefan/7787277/working/3D/308' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497448.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497448.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497448/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497448 none CN1C=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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: [14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 32, 96, 96, 96, 96, 96, 1, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 16, 15, 96, 1, 1, 14] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 40, 23, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41])
total number of confs: 198
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497448 none CN1C=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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, 124, 124, 124, 96, 96, 96, 96, 96, 71, 41, 71, 13, 1, 1, 1, 1, 1, 1, 1, 96, 201, 201, 201, 201, 201, 201, 124, 96, 96, 96, 96, 96, 41, 41, 1, 96, 96, 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])
total number of confs: 524
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497448 none CN1C=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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, 5, 5, 5, 14, 14, 14, 14, 14, 40, 40, 80, 121, 201, 201, 201, 201, 201, 14, 1, 2, 2, 2, 1, 1, 5, 14, 14, 14, 14, 14, 80, 80, 201, 14, 14, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 531
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497448 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497448
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497448/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497448
Building REAL300025497449
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497449'
/scratch/stefan/7787277/working/building/REAL300025497449 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497449

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497449/0 /scratch/stefan/7787277/working/building/REAL300025497449 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 309)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/309
`/scratch/stefan/7787277/working/3D/309' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497449.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497449.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497449/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497449 none CN1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 49, 150, 150, 150, 150, 150, 1, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 25, 25, 150, 1, 1, 15] 201
rigid atoms, others: [32, 33, 34, 38, 7, 8, 9, 10, 11, 12, 13, 23, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40])
total number of confs: 295
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497449 none CN1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 150, 150, 150, 150, 150, 111, 42, 111, 13, 1, 1, 1, 1, 1, 1, 1, 150, 201, 201, 201, 201, 201, 196, 150, 150, 150, 150, 150, 42, 42, 1, 150, 150, 201] 201
rigid atoms, others: [37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 602
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497449 none CN1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 15, 15, 15, 15, 15, 38, 38, 93, 129, 201, 201, 201, 201, 201, 15, 1, 2, 2, 2, 1, 6, 15, 15, 15, 15, 15, 93, 93, 201, 15, 15, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 24, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 545
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497449 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497449
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497449/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497449
Building REAL300025497450
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497450'
/scratch/stefan/7787277/working/building/REAL300025497450 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497450

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497450/0 /scratch/stefan/7787277/working/building/REAL300025497450 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 310)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/310
`/scratch/stefan/7787277/working/3D/310' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1COC(=O)C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497450.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497450.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497450/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497450 none O=C(CC1COC(=O)C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 12, 1, 11, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 25, 46, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 63, 63, 63, 63, 63, 1, 25, 25, 46, 46, 46, 46, 46, 5, 1, 1, 1, 1, 1, 7, 7, 63, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 253
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497450 none O=C(CC1COC(=O)C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 12, 1, 11, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 189, 201, 201, 201, 201, 201, 63, 63, 63, 63, 63, 49, 30, 49, 13, 1, 1, 1, 1, 1, 1, 1, 63, 189, 189, 201, 201, 201, 201, 201, 95, 63, 63, 63, 63, 63, 30, 30, 1, 63, 63] 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])
total number of confs: 792
number of broken/clashed sets: 66
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497450 none O=C(CC1COC(=O)C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 12, 1, 11, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 25, 25, 46, 46, 46, 46, 46, 56, 56, 97, 134, 201, 201, 201, 201, 201, 46, 6, 6, 1, 1, 1, 1, 1, 25, 46, 46, 46, 46, 46, 97, 97, 201, 46, 46] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 566
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497450 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497450
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497450/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497450
Building REAL300025497451
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497451'
/scratch/stefan/7787277/working/building/REAL300025497451 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497451

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497451/0 /scratch/stefan/7787277/working/building/REAL300025497451 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 311)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/311
`/scratch/stefan/7787277/working/3D/311' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)OC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497451.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497451.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497451/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497451 none CC1=C(C)OC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 12, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 56, 145, 145, 145, 145, 145, 1, 11, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 32, 32, 145, 1, 1, 11] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 302
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497451 none CC1=C(C)OC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 12, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 199, 199, 199, 145, 145, 145, 145, 145, 107, 45, 107, 13, 1, 1, 1, 1, 1, 1, 1, 145, 201, 201, 201, 201, 201, 201, 201, 199, 145, 145, 145, 145, 145, 45, 45, 1, 145, 145, 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])
total number of confs: 606
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497451 none CC1=C(C)OC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 12, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 34, 34, 91, 127, 201, 201, 201, 201, 201, 11, 1, 2, 2, 2, 1, 1, 1, 4, 11, 11, 11, 11, 11, 91, 91, 201, 11, 11, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 43, 25, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 545
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497451 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497451
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497451/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497451
Building REAL300025497452
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497452'
/scratch/stefan/7787277/working/building/REAL300025497452 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497452

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497452/0 /scratch/stefan/7787277/working/building/REAL300025497452 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 312)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/312
`/scratch/stefan/7787277/working/3D/312' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CC=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497452.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497452.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497452/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497452 none O=C(CC1=CC=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 16, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 21, 47, 47, 47, 47, 47, 1, 16, 16, 30, 30, 30, 30, 5, 1, 1, 1, 1, 1, 14, 14, 47, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 182
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497452 none O=C(CC1=CC=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 132, 201, 201, 201, 201, 201, 47, 47, 47, 47, 47, 45, 32, 45, 13, 1, 1, 1, 1, 1, 1, 1, 47, 132, 132, 201, 201, 201, 201, 61, 47, 47, 47, 47, 47, 32, 32, 1, 47, 47] 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])
total number of confs: 672
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497452 none O=C(CC1=CC=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 1, 11, 11, 30, 30, 30, 30, 30, 57, 57, 99, 132, 201, 201, 201, 201, 201, 30, 4, 4, 1, 1, 1, 1, 11, 30, 30, 30, 30, 30, 99, 99, 201, 30, 30] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 561
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497452 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497452
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497452/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497452
Building REAL300025497453
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497453'
/scratch/stefan/7787277/working/building/REAL300025497453 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497453

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497453/0 /scratch/stefan/7787277/working/building/REAL300025497453 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 313)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/313
`/scratch/stefan/7787277/working/3D/313' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCCO2)C1)

`REAL300025497453.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497453.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497453/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497453 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 17, 38, 111, 111, 111, 111, 111, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 16, 1, 17, 17, 111, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 201
rigid atoms, others: [32, 1, 43, 44, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 228
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497453 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 16, 42, 82, 127, 201, 201, 201, 201, 201, 16, 16, 16, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 82, 82, 201, 16, 16, 16, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 201
rigid atoms, others: [34, 35, 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, 43, 44])
total number of confs: 512
number of broken/clashed sets: 32
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497453 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 7, 7, 6, 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, 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, 39, 13, 1, 1, 1, 1, 1, 1, 1, 78, 111, 111, 111, 111, 111, 172, 172, 172, 201, 201, 201, 201, 201, 111, 39, 39, 1, 111, 111, 111, 111, 111, 172, 201, 201, 201, 201, 201, 201, 201, 201, 201, 111, 111] 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: 646
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497453 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497453
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497453/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497453
Building REAL300025497454
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497454'
/scratch/stefan/7787277/working/building/REAL300025497454 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497454

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497454/0 /scratch/stefan/7787277/working/building/REAL300025497454 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 314)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/314
`/scratch/stefan/7787277/working/3D/314' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O)

`REAL300025497454.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497454.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497454/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497454 none CC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [25, 25, 25, 25, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 37, 99, 99, 99, 99, 99, 1, 25, 25, 25, 25, 25, 25, 25, 5, 1, 1, 1, 1, 1, 20, 20, 99, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 250
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497454 none CC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 136, 136, 136, 99, 99, 99, 99, 99, 80, 41, 80, 13, 1, 1, 1, 1, 1, 1, 1, 99, 201, 201, 201, 201, 201, 201, 201, 136, 99, 99, 99, 99, 99, 41, 41, 1, 99, 99] 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])
total number of confs: 650
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497454 none CC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 11, 11, 25, 25, 25, 25, 25, 53, 53, 90, 131, 201, 201, 201, 201, 201, 25, 1, 1, 2, 2, 2, 1, 1, 11, 25, 25, 25, 25, 25, 90, 90, 201, 25, 25] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 528
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497454 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497454
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497454/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497454
Building REAL300025497455
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497455'
/scratch/stefan/7787277/working/building/REAL300025497455 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497455

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497455/0 /scratch/stefan/7787277/working/building/REAL300025497455 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 315)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/315
`/scratch/stefan/7787277/working/3D/315' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(SC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497455.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497455.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497455/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497455 none CCC(SC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [175, 174, 96, 174, 201, 96, 96, 52, 52, 52, 52, 52, 52, 47, 52, 13, 1, 1, 1, 1, 1, 1, 1, 52, 175, 175, 175, 175, 175, 174, 201, 201, 201, 96, 52, 52, 52, 52, 52, 47, 47, 1, 52, 52] 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])
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: REAL300025497455 none CCC(SC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 14, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [30, 19, 5, 19, 38, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 11, 52, 52, 52, 52, 52, 1, 30, 30, 30, 30, 30, 19, 38, 38, 38, 5, 1, 1, 1, 1, 1, 7, 7, 52, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 244
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497455 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497455
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497455/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497455
Building REAL300025497456
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497456'
/scratch/stefan/7787277/working/building/REAL300025497456 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497456

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497456/0 /scratch/stefan/7787277/working/building/REAL300025497456 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 316)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/316
`/scratch/stefan/7787277/working/3D/316' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NC=N1)

`REAL300025497456.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497456.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497456/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497456 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 6, 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, 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: [14, 14, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 52, 141, 141, 141, 141, 141, 1, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 28, 28, 141, 1, 1, 14] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41])
total number of confs: 292
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497456 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 6, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 199, 199, 199, 141, 141, 141, 141, 141, 105, 42, 105, 13, 1, 1, 1, 1, 1, 1, 1, 141, 201, 201, 201, 201, 201, 201, 201, 199, 141, 141, 141, 141, 141, 42, 42, 1, 141, 141, 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])
total number of confs: 618
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497456 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 6, 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, 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, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 36, 36, 86, 130, 201, 201, 201, 201, 201, 14, 1, 1, 1, 2, 2, 2, 1, 6, 14, 14, 14, 14, 14, 86, 86, 201, 14, 14, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 41, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 523
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497456 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497456
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497456/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497456
Building REAL300025497457
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497457'
/scratch/stefan/7787277/working/building/REAL300025497457 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497457

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497457/0 /scratch/stefan/7787277/working/building/REAL300025497457 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 317)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/317
`/scratch/stefan/7787277/working/3D/317' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497457.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497457.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497457/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497457 none CC1(C)CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 28, 101, 101, 101, 101, 101, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 14, 14, 101, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 205
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497457 none CC1(C)CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 148, 148, 148, 101, 101, 101, 101, 101, 80, 41, 80, 13, 1, 1, 1, 1, 1, 1, 1, 101, 201, 201, 201, 201, 201, 201, 201, 201, 201, 148, 101, 101, 101, 101, 101, 41, 41, 1, 101, 101] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43])
total number of confs: 668
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497457 none CC1(C)CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 5, 5, 5, 13, 13, 13, 13, 13, 41, 41, 77, 117, 201, 201, 201, 201, 201, 13, 2, 2, 2, 2, 2, 2, 1, 1, 1, 5, 13, 13, 13, 13, 13, 77, 77, 201, 13, 13] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 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, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 517
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497457 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497457
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497457/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497457
Building REAL300025497458
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497458'
/scratch/stefan/7787277/working/building/REAL300025497458 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497458

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497458/0 /scratch/stefan/7787277/working/building/REAL300025497458 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 318)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/318
`/scratch/stefan/7787277/working/3D/318' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)OCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497458.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497458.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497458/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497458 none CCC(C)OCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 197, 147, 147, 147, 95, 95, 95, 95, 95, 72, 31, 72, 13, 1, 1, 1, 1, 1, 1, 1, 95, 201, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 147, 95, 95, 95, 95, 95, 31, 31, 1, 95, 95] 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])
total number of confs: 742
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: REAL300025497458 none CCC(C)OCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [32, 32, 29, 32, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 19, 95, 95, 95, 95, 95, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 13, 13, 5, 1, 1, 1, 1, 1, 9, 9, 95, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 226
number of broken/clashed sets: 83
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497458 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497458
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497458/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497458
Building REAL300025497459
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497459'
/scratch/stefan/7787277/working/building/REAL300025497459 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497459

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497459/0 /scratch/stefan/7787277/working/building/REAL300025497459 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 319)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/319
`/scratch/stefan/7787277/working/3D/319' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)C[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497459.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497459.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497459/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497459 none CC1(C)C[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 29, 102, 102, 102, 102, 102, 1, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 14, 14, 102, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 206
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497459 none CC1(C)C[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 201, 148, 148, 102, 102, 102, 102, 102, 80, 40, 80, 12, 1, 1, 1, 1, 1, 1, 1, 102, 201, 201, 201, 201, 201, 201, 201, 201, 148, 102, 102, 102, 102, 102, 40, 40, 1, 102, 102] 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])
total number of confs: 669
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497459 none CC1(C)C[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 40, 40, 75, 115, 201, 201, 201, 201, 201, 13, 2, 2, 2, 2, 2, 2, 1, 1, 5, 13, 13, 13, 13, 13, 75, 75, 201, 13, 13] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 512
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497459 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497459
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497459/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497459
Building REAL300025497460
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497460'
/scratch/stefan/7787277/working/building/REAL300025497460 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497460

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497460/0 /scratch/stefan/7787277/working/building/REAL300025497460 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 320)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/320
`/scratch/stefan/7787277/working/3D/320' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(O)(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1)

`REAL300025497460.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497460.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497460/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497460 none CC(O)(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 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, 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]
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, 181, 201, 103, 103, 103, 70, 70, 70, 70, 70, 56, 31, 56, 13, 1, 1, 1, 1, 1, 1, 1, 70, 200, 201, 201, 201, 201, 201, 603, 181, 181, 103, 70, 70, 70, 70, 70, 31, 31, 1, 70, 70, 201, 201, 201, 201, 201] 603
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: 1414
number of broken/clashed sets: 215
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497460 none CC(O)(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 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, 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]
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, 9, 15, 15, 15, 29, 29, 29, 29, 29, 45, 45, 82, 124, 201, 201, 201, 201, 201, 29, 1, 1, 1, 3, 3, 3, 9, 9, 9, 15, 29, 29, 29, 29, 29, 82, 82, 201, 29, 29, 1, 1, 1, 1, 1] 603
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: 547
number of broken/clashed sets: 215
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497460 none CC(O)(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 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, 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]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [25, 21, 27, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 19, 70, 70, 70, 70, 70, 1, 26, 29, 29, 27, 27, 27, 81, 21, 21, 5, 1, 1, 1, 1, 1, 10, 10, 70, 1, 1, 29, 29, 29, 29, 29] 603
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47])
total number of confs: 322
number of broken/clashed sets: 215
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497460 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497460
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497460/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497460
Building REAL300025497461
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497461'
/scratch/stefan/7787277/working/building/REAL300025497461 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497461

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497461/0 /scratch/stefan/7787277/working/building/REAL300025497461 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 321)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/321
`/scratch/stefan/7787277/working/3D/321' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CSC(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497461.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497461.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497461/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497461 none CSC(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 181, 168, 181, 97, 97, 97, 80, 80, 80, 80, 80, 63, 31, 63, 13, 1, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 181, 181, 181, 181, 168, 168, 97, 80, 80, 80, 80, 80, 31, 31, 1, 80, 80] 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])
total number of confs: 766
number of broken/clashed sets: 80
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497461 none CSC(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 14, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [26, 18, 14, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 14, 80, 80, 80, 80, 80, 1, 26, 26, 26, 18, 18, 18, 18, 14, 14, 4, 1, 1, 1, 1, 1, 7, 7, 80, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 197
number of broken/clashed sets: 80
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497461 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497461
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497461/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497461
Building REAL300025497462
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497462'
/scratch/stefan/7787277/working/building/REAL300025497462 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497462

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497462/0 /scratch/stefan/7787277/working/building/REAL300025497462 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 322)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/322
`/scratch/stefan/7787277/working/3D/322' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497462.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497462.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497462/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497462 none O=C(CN1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 1, 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, 6, 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: [5, 5, 5, 16, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 26, 94, 94, 94, 94, 94, 1, 16, 16, 19, 19, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 15, 15, 94, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 219
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497462 none O=C(CN1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 1, 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, 6, 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: [129, 129, 129, 201, 201, 201, 201, 201, 201, 94, 94, 94, 94, 94, 59, 31, 59, 13, 1, 1, 1, 1, 1, 1, 1, 94, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 94, 94, 94, 94, 94, 31, 31, 1, 94, 94] 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])
total number of confs: 804
number of broken/clashed sets: 45
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497462 none O=C(CN1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 1, 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, 6, 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: [10, 5, 1, 1, 1, 1, 1, 1, 1, 10, 10, 19, 19, 19, 19, 19, 49, 49, 80, 117, 201, 201, 201, 201, 201, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 10, 19, 19, 19, 19, 19, 80, 80, 201, 19, 19] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 505
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497462 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497462
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497462/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497462
Building REAL300025497463
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497463'
/scratch/stefan/7787277/working/building/REAL300025497463 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497463

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497463/0 /scratch/stefan/7787277/working/building/REAL300025497463 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 323)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/323
`/scratch/stefan/7787277/working/3D/323' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2CCCO2)C1)

`REAL300025497463.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497463.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497463/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497463 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2CCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 17, 35, 107, 107, 107, 107, 107, 1, 1, 1, 1, 1, 1, 4, 4, 4, 18, 18, 18, 18, 18, 1, 17, 17, 107, 1, 1, 1, 1, 1, 4, 18, 18, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 40, 41, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 230
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497463 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2CCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 18, 43, 84, 124, 201, 201, 201, 201, 201, 18, 18, 18, 18, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 18, 84, 84, 201, 18, 18, 18, 18, 18, 10, 1, 1, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [34, 35, 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, 40, 41])
total number of confs: 508
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497463 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2CCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 39, 12, 1, 1, 1, 1, 1, 1, 1, 76, 107, 107, 107, 107, 107, 160, 160, 160, 201, 201, 201, 201, 201, 107, 39, 39, 1, 107, 107, 107, 107, 107, 160, 201, 201, 201, 201, 201, 201, 107, 107] 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: 653
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497463 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497463
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497463/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497463
Building REAL300025497464
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497464'
/scratch/stefan/7787277/working/building/REAL300025497464 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497464

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497464/0 /scratch/stefan/7787277/working/building/REAL300025497464 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 324)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/324
`/scratch/stefan/7787277/working/3D/324' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=NC=N1)

`REAL300025497464.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497464.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497464/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497464 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 153, 153, 153, 107, 107, 107, 107, 107, 60, 30, 60, 13, 1, 1, 1, 1, 1, 1, 1, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201, 153, 107, 107, 107, 107, 107, 30, 30, 1, 107, 107, 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])
total number of confs: 707
number of broken/clashed sets: 70
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497464 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 17, 17, 17, 33, 33, 33, 33, 33, 50, 50, 87, 130, 201, 201, 201, 201, 201, 33, 1, 1, 1, 1, 1, 10, 10, 10, 10, 17, 33, 33, 33, 33, 33, 87, 87, 201, 33, 33, 1, 1] 201
rigid atoms, others: [1, 41, 42, 21, 22, 23, 24, 25] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 533
number of broken/clashed sets: 70
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497464 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 28, 107, 107, 107, 107, 107, 1, 21, 33, 33, 33, 33, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 15, 14, 107, 1, 1, 33, 33] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 20, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42])
total number of confs: 271
number of broken/clashed sets: 70
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497464 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497464
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497464/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497464
Building REAL300025497465
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497465'
/scratch/stefan/7787277/working/building/REAL300025497465 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497465

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497465/0 /scratch/stefan/7787277/working/building/REAL300025497465 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 325)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/325
`/scratch/stefan/7787277/working/3D/325' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCOCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497465.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497465.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497465/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497465 none CN1CCOCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 31, 50, 131, 131, 131, 131, 131, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 31, 31, 131, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 292
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497465 none CN1CCOCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 190, 190, 190, 131, 131, 131, 131, 131, 98, 43, 98, 13, 1, 1, 1, 1, 1, 1, 1, 131, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 190, 131, 131, 131, 131, 131, 43, 43, 1, 131, 131] 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])
total number of confs: 636
number of broken/clashed sets: 24
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497465 none CN1CCOCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 11, 11, 11, 11, 11, 35, 35, 92, 125, 201, 201, 201, 201, 201, 11, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 92, 92, 201, 11, 11] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 33, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 557
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497465 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497465
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497465/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497465
Building REAL300025497466
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497466'
/scratch/stefan/7787277/working/building/REAL300025497466 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497466

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497466/0 /scratch/stefan/7787277/working/building/REAL300025497466 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 326)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/326
`/scratch/stefan/7787277/working/3D/326' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NSC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497466.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497466.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497466/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497466 none CC1=NSC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 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, 6, 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: [19, 19, 19, 19, 18, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 26, 100, 100, 100, 100, 100, 1, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 11, 11, 100, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 39, 8, 9, 10, 11, 12, 13, 14, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 191
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497466 none CC1=NSC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 125, 125, 125, 100, 100, 100, 100, 100, 82, 46, 82, 13, 1, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 125, 100, 100, 100, 100, 100, 46, 46, 1, 100, 100] 201
rigid atoms, others: [37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 540
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497466 none CC1=NSC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 14, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 19, 19, 19, 37, 37, 70, 113, 201, 201, 201, 201, 201, 19, 2, 2, 2, 1, 9, 19, 19, 19, 19, 19, 70, 70, 201, 19, 19] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 501
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497466 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497466
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497466/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497466
Building REAL300025497467
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497467'
/scratch/stefan/7787277/working/building/REAL300025497467 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497467

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497467/0 /scratch/stefan/7787277/working/building/REAL300025497467 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 327)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/327
`/scratch/stefan/7787277/working/3D/327' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497467.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497467.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497467/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497467 none C#CCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 181, 169, 155, 53, 53, 53, 37, 37, 37, 37, 37, 36, 27, 36, 13, 1, 1, 1, 1, 1, 1, 1, 37, 201, 201, 201, 181, 181, 181, 181, 155, 155, 53, 37, 37, 37, 37, 37, 27, 27, 1, 37, 37] 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])
total number of confs: 933
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: REAL300025497467 none C#CCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [42, 42, 26, 24, 20, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 37, 37, 37, 37, 37, 1, 42, 42, 42, 26, 26, 26, 26, 20, 20, 4, 1, 1, 1, 1, 1, 5, 5, 37, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 250
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497467 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497467
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497467/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497467
Building REAL300025497468
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497468'
/scratch/stefan/7787277/working/building/REAL300025497468 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497468

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497468/0 /scratch/stefan/7787277/working/building/REAL300025497468 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 328)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/328
`/scratch/stefan/7787277/working/3D/328' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCNC(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497468.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497468.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497468/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497468 none C#CCNC(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
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, 195, 175, 195, 72, 72, 72, 71, 71, 71, 71, 71, 54, 30, 54, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 195, 175, 175, 72, 71, 71, 71, 71, 71, 30, 30, 1, 71, 71] 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])
total number of confs: 758
number of broken/clashed sets: 104
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497468 none C#CCNC(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 8, 1, 11, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 19, 19, 10, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 15, 71, 71, 71, 71, 71, 1, 37, 37, 37, 19, 10, 10, 3, 1, 1, 1, 1, 1, 8, 8, 71, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 261
number of broken/clashed sets: 104
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497468 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497468
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497468/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497468
Building REAL300025497469
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497469'
/scratch/stefan/7787277/working/building/REAL300025497469 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497469

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497469/0 /scratch/stefan/7787277/working/building/REAL300025497469 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 329)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/329
`/scratch/stefan/7787277/working/3D/329' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCNC(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497469.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497469.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497469/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497469 none CCNC(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 156, 163, 73, 73, 73, 69, 69, 69, 69, 69, 47, 29, 47, 13, 1, 1, 1, 1, 1, 1, 1, 69, 201, 201, 201, 201, 201, 163, 156, 156, 73, 69, 69, 69, 69, 69, 29, 29, 1, 69, 69] 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])
total number of confs: 840
number of broken/clashed sets: 112
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497469 none CCNC(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 19, 10, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 14, 69, 69, 69, 69, 69, 1, 37, 37, 37, 37, 37, 19, 10, 10, 4, 1, 1, 1, 1, 1, 8, 8, 69, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 258
number of broken/clashed sets: 112
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497469 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497469
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497469/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497469
Building REAL300025497470
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497470'
/scratch/stefan/7787277/working/building/REAL300025497470 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497470

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497470/0 /scratch/stefan/7787277/working/building/REAL300025497470 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 330)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/330
`/scratch/stefan/7787277/working/3D/330' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497470.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497470.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497470/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497470 none CNC(=O)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 200, 201, 152, 151, 61, 61, 61, 53, 53, 53, 53, 53, 43, 25, 43, 12, 1, 1, 1, 1, 1, 1, 1, 53, 201, 201, 201, 201, 185, 189, 177, 177, 151, 151, 61, 53, 53, 53, 53, 53, 25, 25, 1, 53, 53] 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])
total number of confs: 959
number of broken/clashed sets: 159
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497470 none CNC(=O)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 34, 39, 16, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 15, 53, 53, 53, 53, 53, 1, 39, 39, 39, 39, 31, 32, 20, 20, 12, 12, 4, 1, 1, 1, 1, 1, 9, 9, 53, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 278
number of broken/clashed sets: 159
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497470 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497470
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497470/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497470
Building REAL300025497471
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497471'
/scratch/stefan/7787277/working/building/REAL300025497471 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497471

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497471/0 /scratch/stefan/7787277/working/building/REAL300025497471 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 331)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/331
`/scratch/stefan/7787277/working/3D/331' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497471.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497471.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497471/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497471 none COC1=NOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 54, 141, 141, 141, 141, 141, 1, 12, 16, 16, 16, 5, 1, 1, 1, 1, 1, 32, 32, 141, 1, 1, 12] 201
rigid atoms, others: [32, 33, 34, 38, 39, 8, 9, 10, 11, 12, 13, 14, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37, 40])
total number of confs: 303
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497471 none COC1=NOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 141, 141, 141, 141, 141, 102, 47, 102, 13, 1, 1, 1, 1, 1, 1, 1, 141, 201, 201, 201, 201, 190, 141, 141, 141, 141, 141, 47, 47, 1, 141, 141, 201] 201
rigid atoms, others: [37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 597
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497471 none COC1=NOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 32, 32, 83, 113, 201, 201, 201, 201, 201, 12, 1, 2, 2, 2, 4, 12, 12, 12, 12, 12, 83, 83, 201, 12, 12, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 40, 25] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 504
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497471 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497471
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497471/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497471
Building REAL300025497472
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497472'
/scratch/stefan/7787277/working/building/REAL300025497472 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497472

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497472/0 /scratch/stefan/7787277/working/building/REAL300025497472 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 332)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/332
`/scratch/stefan/7787277/working/3D/332' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497472.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497472.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497472/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497472 none COC(C)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
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, 199, 126, 126, 126, 83, 83, 83, 83, 83, 67, 30, 67, 13, 1, 1, 1, 1, 1, 1, 1, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 126, 83, 83, 83, 83, 83, 30, 30, 1, 83, 83] 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])
total number of confs: 812
number of broken/clashed sets: 75
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497472 none COC(C)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 20, 22, 19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 18, 83, 83, 83, 83, 83, 1, 22, 22, 22, 22, 22, 22, 22, 21, 21, 19, 19, 5, 1, 1, 1, 1, 1, 9, 9, 83, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 215
number of broken/clashed sets: 75
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497472 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497472
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497472/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497472
Building REAL300025497473
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497473'
/scratch/stefan/7787277/working/building/REAL300025497473 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497473

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497473/0 /scratch/stefan/7787277/working/building/REAL300025497473 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 333)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/333
`/scratch/stefan/7787277/working/3D/333' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1)

`REAL300025497473.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497473.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497473/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497473 none CCC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 36, 101, 101, 101, 101, 101, 1, 5, 5, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 19, 19, 101, 1, 1, 5] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42])
total number of confs: 259
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497473 none CCC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 124, 124, 124, 124, 124, 124, 101, 101, 101, 101, 101, 80, 41, 80, 13, 1, 1, 1, 1, 1, 1, 1, 101, 124, 124, 201, 201, 201, 201, 201, 124, 101, 101, 101, 101, 101, 41, 41, 1, 101, 101, 124] 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: 856
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497473 none CCC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 1, 1, 5, 5, 5, 5, 5, 15, 15, 38, 60, 124, 124, 124, 124, 124, 5, 1, 1, 9, 9, 9, 9, 9, 1, 5, 5, 5, 5, 5, 38, 38, 124, 5, 5, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 42, 24, 25, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 313
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497473 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497473
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497473/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497473
Building REAL300025497474
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497474'
/scratch/stefan/7787277/working/building/REAL300025497474 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497474

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497474/0 /scratch/stefan/7787277/working/building/REAL300025497474 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 334)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/334
`/scratch/stefan/7787277/working/3D/334' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)C=N2)C1)

`REAL300025497474.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497474.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497474/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497474 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)C=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 21, 46, 133, 133, 133, 133, 133, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 1, 21, 21, 133, 1, 1, 1, 1, 1, 5, 8, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37])
total number of confs: 249
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497474 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)C=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 8, 24, 56, 97, 201, 201, 201, 201, 201, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 8, 56, 56, 201, 8, 8, 8, 8, 8, 3, 1, 1, 1, 8, 8] 201
rigid atoms, others: [35, 36, 37, 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, 38, 39])
total number of confs: 434
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497474 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)C=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [97, 40, 13, 1, 1, 1, 1, 1, 1, 1, 97, 133, 133, 133, 133, 133, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 40, 40, 1, 133, 133, 133, 133, 133, 201, 201, 201, 201, 133, 133] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 631
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497474 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497474
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497474/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497474
Building REAL300025497475
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497475'
/scratch/stefan/7787277/working/building/REAL300025497475 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497475

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497475/0 /scratch/stefan/7787277/working/building/REAL300025497475 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 335)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/335
`/scratch/stefan/7787277/working/3D/335' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1N)

`REAL300025497475.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497475.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497475/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497475 none CN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [19, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 37, 100, 100, 100, 100, 100, 1, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 21, 21, 100, 1, 1, 19, 19] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 40, 23, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42])
total number of confs: 223
number of broken/clashed sets: 80
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497475 none CN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 138, 138, 138, 100, 100, 100, 100, 100, 78, 40, 78, 13, 1, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 201, 201, 138, 100, 100, 100, 100, 100, 40, 40, 1, 100, 100, 201, 201] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 542
number of broken/clashed sets: 80
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497475 none CN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 19, 19, 19, 19, 47, 47, 97, 130, 201, 201, 201, 201, 201, 19, 1, 1, 2, 2, 2, 1, 6, 19, 19, 19, 19, 19, 97, 97, 201, 19, 19, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 562
number of broken/clashed sets: 80
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497475 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497475
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497475/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497475
Building REAL300025497476
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497476'
/scratch/stefan/7787277/working/building/REAL300025497476 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497476

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497476/0 /scratch/stefan/7787277/working/building/REAL300025497476 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 336)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/336
`/scratch/stefan/7787277/working/3D/336' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CN=C2)C1)

`REAL300025497476.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497476.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497476/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497476 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 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, 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: [5, 1, 5, 17, 37, 134, 134, 134, 134, 134, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 1, 17, 17, 134, 1, 1, 1, 1, 1, 5, 9, 9, 9, 1, 1] 201
rigid atoms, others: [32, 1, 37, 38, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36])
total number of confs: 241
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497476 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 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, 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: [39, 12, 39, 81, 129, 201, 201, 201, 201, 201, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 12, 81, 81, 201, 12, 12, 12, 12, 12, 4, 1, 1, 1, 12, 12] 201
rigid atoms, others: [34, 35, 36, 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, 37, 38])
total number of confs: 514
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497476 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 5, 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, 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: [95, 48, 13, 1, 1, 1, 1, 1, 1, 1, 95, 134, 134, 134, 134, 134, 201, 201, 201, 201, 201, 201, 201, 201, 134, 48, 48, 1, 134, 134, 134, 134, 134, 201, 201, 201, 201, 134, 134] 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: 631
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497476 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497476
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497476/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497476
Building REAL300025497477
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497477'
/scratch/stefan/7787277/working/building/REAL300025497477 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497477

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497477/0 /scratch/stefan/7787277/working/building/REAL300025497477 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 337)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/337
`/scratch/stefan/7787277/working/3D/337' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CCOCC2)C1)

`REAL300025497477.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497477.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497477/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497477 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CCOCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 5, 7, 7, 6, 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, 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, 14, 28, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 19, 19, 1, 14, 14, 117, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [32, 1, 41, 10, 11, 12, 13, 14, 15, 42, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 211
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497477 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CCOCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 5, 7, 7, 6, 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, 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: [47, 19, 47, 87, 124, 201, 201, 201, 201, 201, 19, 19, 19, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 19, 87, 87, 201, 19, 19, 19, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [34, 35, 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, 41, 42])
total number of confs: 531
number of broken/clashed sets: 31
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497477 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CCOCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 12, 5, 5, 5, 7, 7, 6, 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, 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: [81, 45, 13, 1, 1, 1, 1, 1, 1, 1, 81, 117, 117, 117, 117, 117, 168, 168, 168, 201, 201, 201, 201, 201, 117, 45, 45, 1, 117, 117, 117, 117, 117, 168, 201, 201, 201, 201, 201, 201, 201, 117, 117] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 595
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497477 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497477
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497477/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497477
Building REAL300025497478
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497478'
/scratch/stefan/7787277/working/building/REAL300025497478 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497478

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497478/0 /scratch/stefan/7787277/working/building/REAL300025497478 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 338)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/338
`/scratch/stefan/7787277/working/3D/338' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=COC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497478.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497478.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497478/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497478 none O=C(CC1=COC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 12, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 21, 51, 51, 51, 51, 51, 1, 14, 14, 26, 26, 26, 5, 1, 1, 1, 1, 1, 14, 14, 51, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 179
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497478 none O=C(CC1=COC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 12, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 117, 201, 201, 201, 201, 51, 51, 51, 51, 51, 49, 34, 49, 13, 1, 1, 1, 1, 1, 1, 1, 51, 117, 117, 201, 201, 201, 63, 51, 51, 51, 51, 51, 34, 34, 1, 51, 51] 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])
total number of confs: 648
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497478 none O=C(CC1=COC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 12, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 26, 26, 26, 26, 26, 53, 53, 96, 131, 201, 201, 201, 201, 201, 26, 2, 2, 1, 1, 1, 9, 26, 26, 26, 26, 26, 96, 96, 201, 26, 26] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 554
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497478 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497478
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497478/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497478
Building REAL300025497479
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497479'
/scratch/stefan/7787277/working/building/REAL300025497479 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497479

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497479/0 /scratch/stefan/7787277/working/building/REAL300025497479 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 339)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/339
`/scratch/stefan/7787277/working/3D/339' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1)

`REAL300025497479.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497479.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497479/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497479 none CC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 35, 62, 150, 150, 150, 150, 150, 1, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 35, 35, 150, 1, 1, 11] 201
rigid atoms, others: [32, 33, 37, 6, 7, 8, 9, 10, 11, 12, 22, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39])
total number of confs: 319
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497479 none CC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 150, 150, 150, 150, 150, 108, 45, 108, 13, 1, 1, 1, 1, 1, 1, 1, 150, 201, 201, 201, 201, 201, 201, 150, 150, 150, 150, 150, 45, 45, 1, 150, 150, 201] 201
rigid atoms, others: [36, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39])
total number of confs: 603
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497479 none CC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 3, 11, 11, 11, 11, 11, 32, 32, 87, 122, 201, 201, 201, 201, 201, 11, 1, 1, 2, 2, 2, 4, 11, 11, 11, 11, 11, 87, 87, 201, 11, 11, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 39, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 536
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497479 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497479
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497479/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497479
Building REAL300025497480
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497480'
/scratch/stefan/7787277/working/building/REAL300025497480 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497480

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497480/0 /scratch/stefan/7787277/working/building/REAL300025497480 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 340)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/340
`/scratch/stefan/7787277/working/3D/340' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CCCCCC2)C1)

`REAL300025497480.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497480.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497480/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497480 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CCCCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 21, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 18, 1, 13, 13, 75, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 14, 15, 46, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 157
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497480 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CCCCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 18, 42, 82, 108, 201, 201, 201, 201, 201, 18, 18, 18, 18, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 18, 82, 82, 201, 18, 18, 18, 18, 18, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [35, 36, 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, 46, 47])
total number of confs: 522
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497480 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CCCCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 36, 13, 1, 1, 1, 1, 1, 1, 1, 54, 75, 75, 75, 75, 75, 106, 106, 106, 201, 201, 201, 201, 201, 201, 75, 36, 36, 1, 75, 75, 75, 75, 75, 106, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 75, 75] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 491
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497480 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497480
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497480/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497480
Building REAL300025497481
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497481'
/scratch/stefan/7787277/working/building/REAL300025497481 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497481

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497481/0 /scratch/stefan/7787277/working/building/REAL300025497481 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 341)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/341
`/scratch/stefan/7787277/working/3D/341' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](NC(N)=O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497481.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497481.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497481/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497481 none C[C@H](NC(N)=O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 201, 201, 201, 201, 201, 134, 134, 104, 104, 104, 104, 104, 58, 29, 58, 13, 1, 1, 1, 1, 1, 1, 1, 104, 201, 201, 201, 201, 201, 201, 134, 104, 104, 104, 104, 104, 29, 29, 1, 104, 104] 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])
total number of confs: 740
number of broken/clashed sets: 55
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497481 none C[C@H](NC(N)=O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 4, 15, 15, 25, 25, 25, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 29, 104, 104, 104, 104, 104, 1, 15, 15, 15, 25, 25, 25, 4, 1, 1, 1, 1, 1, 15, 15, 104, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 257
number of broken/clashed sets: 55
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497481 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497481
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497481/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497481
Building REAL300025497482
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497482'
/scratch/stefan/7787277/working/building/REAL300025497482 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497482

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497482/0 /scratch/stefan/7787277/working/building/REAL300025497482 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 342)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/342
`/scratch/stefan/7787277/working/3D/342' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1OCCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497482.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497482.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497482/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497482 none O=C(CC1OCCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 25, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 18, 75, 75, 75, 75, 75, 1, 25, 25, 41, 41, 41, 41, 41, 41, 41, 5, 1, 1, 1, 1, 1, 9, 9, 75, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 257
number of broken/clashed sets: 76
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497482 none O=C(CC1OCCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 201, 201, 75, 75, 75, 75, 75, 54, 29, 54, 13, 1, 1, 1, 1, 1, 1, 1, 75, 198, 198, 201, 201, 201, 201, 201, 201, 201, 119, 75, 75, 75, 75, 75, 29, 29, 1, 75, 75] 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])
total number of confs: 759
number of broken/clashed sets: 76
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497482 none O=C(CC1OCCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 6, 1, 1, 1, 1, 1, 1, 1, 20, 20, 41, 41, 41, 41, 41, 51, 51, 95, 136, 201, 201, 201, 201, 201, 41, 6, 6, 1, 1, 1, 1, 1, 1, 1, 20, 41, 41, 41, 41, 41, 95, 95, 201, 41, 41] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 570
number of broken/clashed sets: 76
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497482 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497482
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497482/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497482
Building REAL300025497483
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497483'
/scratch/stefan/7787277/working/building/REAL300025497483 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497483

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497483/0 /scratch/stefan/7787277/working/building/REAL300025497483 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 343)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/343
`/scratch/stefan/7787277/working/3D/343' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1)

`REAL300025497483.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497483.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497483/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497483 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 6, 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, 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: [12, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 39, 107, 107, 107, 107, 107, 1, 12, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 16, 16, 107, 1, 1, 12] 201
rigid atoms, others: [32, 33, 34, 38, 6, 7, 8, 9, 10, 11, 12, 22, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40])
total number of confs: 207
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497483 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 154, 154, 154, 107, 107, 107, 107, 107, 92, 48, 92, 13, 1, 1, 1, 1, 1, 1, 1, 107, 201, 201, 201, 201, 201, 201, 154, 107, 107, 107, 107, 107, 48, 48, 1, 107, 107, 201] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 591
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497483 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 36, 36, 68, 109, 201, 201, 201, 201, 201, 12, 1, 1, 2, 2, 2, 1, 5, 12, 12, 12, 12, 12, 68, 68, 201, 12, 12, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 40, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 469
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497483 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497483
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497483/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497483
Building REAL300025497484
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497484'
/scratch/stefan/7787277/working/building/REAL300025497484 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497484

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497484/0 /scratch/stefan/7787277/working/building/REAL300025497484 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 344)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/344
`/scratch/stefan/7787277/working/3D/344' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C=C1)

`REAL300025497484.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497484.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497484/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497484 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 1, 7, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 27, 87, 87, 87, 87, 87, 1, 12, 12, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 13, 13, 87, 1, 1, 12, 12, 12, 12, 12] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 21, 39, 38, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44])
total number of confs: 172
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497484 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 1, 7, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 118, 118, 118, 87, 87, 87, 87, 87, 72, 38, 72, 13, 1, 1, 1, 1, 1, 1, 1, 87, 201, 201, 201, 201, 201, 201, 201, 118, 87, 87, 87, 87, 87, 38, 38, 1, 87, 87, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 539
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497484 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 1, 7, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 12, 12, 12, 12, 12, 31, 31, 62, 105, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 2, 2, 2, 5, 12, 12, 12, 12, 12, 62, 62, 201, 12, 12, 2, 2, 2, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 43, 44, 22, 23, 24, 25] set([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: 485
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497484 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497484
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497484/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497484
Building REAL300025497485
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497485'
/scratch/stefan/7787277/working/building/REAL300025497485 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497485

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497485/0 /scratch/stefan/7787277/working/building/REAL300025497485 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 345)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/345
`/scratch/stefan/7787277/working/3D/345' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CN=N1)

`REAL300025497485.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497485.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497485/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497485 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 7, 7, 7, 7, 6, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 29, 82, 82, 82, 82, 82, 1, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 15, 15, 82, 1, 1, 14] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41])
total number of confs: 176
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497485 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 7, 7, 7, 7, 6, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 101, 101, 101, 82, 82, 82, 82, 82, 62, 45, 62, 13, 1, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 201, 201, 201, 201, 101, 82, 82, 82, 82, 82, 45, 45, 1, 82, 82, 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])
total number of confs: 472
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497485 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 7, 7, 7, 7, 6, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 36, 36, 72, 112, 201, 201, 201, 201, 201, 14, 1, 1, 1, 2, 2, 2, 1, 5, 14, 14, 14, 14, 14, 72, 72, 201, 14, 14, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 41, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 512
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497485 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497485
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497485/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497485
Building REAL300025497486
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497486'
/scratch/stefan/7787277/working/building/REAL300025497486 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497486

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497486/0 /scratch/stefan/7787277/working/building/REAL300025497486 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 346)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/346
`/scratch/stefan/7787277/working/3D/346' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCN1C=CN=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497486.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497486.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497486/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497486 none O=C(CCN1C=CN=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 8, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 17, 21, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 30, 90, 90, 90, 90, 90, 1, 17, 17, 21, 21, 32, 32, 5, 1, 1, 1, 1, 1, 17, 17, 90, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 266
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497486 none O=C(CCN1C=CN=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 8, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [110, 110, 110, 196, 200, 201, 201, 201, 201, 90, 90, 90, 90, 90, 51, 27, 51, 13, 1, 1, 1, 1, 1, 1, 1, 90, 196, 196, 200, 200, 201, 201, 110, 90, 90, 90, 90, 90, 27, 27, 1, 90, 90] 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])
total number of confs: 712
number of broken/clashed sets: 54
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497486 none O=C(CCN1C=CN=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 8, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 9, 5, 1, 1, 1, 1, 1, 1, 21, 21, 32, 32, 32, 32, 32, 54, 54, 91, 132, 201, 201, 201, 201, 201, 32, 9, 9, 5, 5, 1, 1, 21, 32, 32, 32, 32, 32, 91, 91, 201, 32, 32] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 561
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497486 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497486
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497486/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497486
Building REAL300025497487
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497487'
/scratch/stefan/7787277/working/building/REAL300025497487 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497487

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497487/0 /scratch/stefan/7787277/working/building/REAL300025497487 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 347)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/347
`/scratch/stefan/7787277/working/3D/347' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497487.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497487.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497487/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497487 none CC(=O)N1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 20, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 25, 59, 59, 59, 59, 59, 1, 20, 30, 30, 30, 20, 20, 20, 5, 1, 1, 1, 1, 1, 15, 15, 59, 1, 1, 20, 20] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44])
total number of confs: 211
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497487 none CC(=O)N1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 169, 201, 169, 169, 75, 75, 75, 59, 59, 59, 59, 59, 52, 34, 52, 13, 1, 1, 1, 1, 1, 1, 1, 59, 169, 201, 201, 201, 169, 169, 169, 75, 59, 59, 59, 59, 59, 34, 34, 1, 59, 59, 169, 169] 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: 675
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497487 none CC(=O)N1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need 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, 2, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 20, 20, 45, 45, 78, 110, 169, 169, 169, 169, 169, 20, 1, 3, 3, 3, 1, 1, 1, 8, 20, 20, 20, 20, 20, 78, 78, 169, 20, 20, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 43, 44, 25, 29, 30, 31] set([0, 2, 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])
total number of confs: 456
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497487 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497487
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497487/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497487
Building REAL300025497488
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497488'
/scratch/stefan/7787277/working/building/REAL300025497488 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497488

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497488/0 /scratch/stefan/7787277/working/building/REAL300025497488 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 348)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/348
`/scratch/stefan/7787277/working/3D/348' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1OC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC1=O)

`REAL300025497488.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497488.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497488/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497488 none CN1OC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 11, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 18, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 52, 124, 124, 124, 124, 124, 1, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 28, 28, 124, 1, 1, 19] 201
rigid atoms, others: [32, 33, 34, 38, 6, 7, 8, 9, 10, 11, 12, 22, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40])
total number of confs: 276
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497488 none CN1OC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 11, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 179, 179, 179, 124, 124, 124, 124, 124, 96, 42, 96, 13, 1, 1, 1, 1, 1, 1, 1, 124, 201, 201, 201, 201, 201, 201, 179, 124, 124, 124, 124, 124, 42, 42, 1, 124, 124, 201] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 609
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497488 none CN1OC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 11, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 19, 19, 47, 47, 101, 133, 201, 201, 201, 201, 201, 19, 1, 1, 1, 2, 2, 2, 7, 19, 19, 19, 19, 19, 101, 101, 201, 19, 19, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 40, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 549
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497488 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497488
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497488/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497488
Building REAL300025497489
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497489'
/scratch/stefan/7787277/working/building/REAL300025497489 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497489

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497489/0 /scratch/stefan/7787277/working/building/REAL300025497489 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 349)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/349
`/scratch/stefan/7787277/working/3D/349' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497489.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497489.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497489/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497489 none CCC(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 201, 192, 201, 78, 78, 78, 45, 45, 45, 45, 45, 41, 30, 41, 13, 1, 1, 1, 1, 1, 1, 1, 45, 201, 201, 201, 201, 201, 201, 201, 201, 201, 192, 192, 78, 45, 45, 45, 45, 45, 30, 30, 1, 45, 45] 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])
total number of confs: 794
number of broken/clashed sets: 65
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497489 none CCC(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [38, 36, 21, 36, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 45, 45, 45, 45, 45, 1, 38, 38, 38, 38, 38, 36, 36, 36, 36, 21, 21, 4, 1, 1, 1, 1, 1, 5, 5, 45, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 233
number of broken/clashed sets: 65
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497489 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497489
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497489/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497489
Building REAL300025497490
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497490'
/scratch/stefan/7787277/working/building/REAL300025497490 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497490

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497490/0 /scratch/stefan/7787277/working/building/REAL300025497490 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 350)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/350
`/scratch/stefan/7787277/working/3D/350' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1)

`REAL300025497490.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497490.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497490/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497490 none COC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 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]
0  hydrogens 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, 29, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 11, 22, 77, 77, 77, 77, 77, 1, 29, 29, 29, 30, 30, 30, 21, 21, 5, 1, 1, 1, 1, 1, 11, 11, 77, 1, 1, 29, 29, 29, 29, 29, 29] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47])
total number of confs: 224
number of broken/clashed sets: 58
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497490 none COC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
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, 111, 111, 111, 77, 77, 77, 77, 77, 57, 30, 57, 13, 1, 1, 1, 1, 1, 1, 1, 77, 201, 201, 201, 201, 201, 201, 190, 190, 111, 77, 77, 77, 77, 77, 30, 30, 1, 77, 77, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 786
number of broken/clashed sets: 58
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497490 none COC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 7, 15, 15, 15, 29, 29, 29, 29, 29, 43, 43, 82, 122, 201, 201, 201, 201, 201, 29, 1, 1, 1, 4, 4, 4, 7, 7, 15, 29, 29, 29, 29, 29, 82, 82, 201, 29, 29, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 2, 3, 42, 43, 44, 45, 46, 47, 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])
total number of confs: 543
number of broken/clashed sets: 58
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497490 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497490
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497490/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497490
Building REAL300025497491
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497491'
/scratch/stefan/7787277/working/building/REAL300025497491 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497491

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497491/0 /scratch/stefan/7787277/working/building/REAL300025497491 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 351)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/351
`/scratch/stefan/7787277/working/3D/351' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1OCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497491.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497491.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497491/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497491 none CC1OCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 50, 139, 139, 139, 139, 139, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 29, 29, 139, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 291
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497491 none CC1OCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 178, 178, 178, 139, 139, 139, 139, 139, 108, 43, 108, 13, 1, 1, 1, 1, 1, 1, 1, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 178, 139, 139, 139, 139, 139, 43, 43, 1, 139, 139] 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])
total number of confs: 635
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497491 none CC1OCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 11, 11, 11, 11, 11, 35, 35, 89, 124, 201, 201, 201, 201, 201, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 89, 89, 201, 11, 11] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 27, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 533
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497491 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497491
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497491/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497491
Building REAL300025497492
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497492'
/scratch/stefan/7787277/working/building/REAL300025497492 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497492

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497492/0 /scratch/stefan/7787277/working/building/REAL300025497492 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 352)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/352
`/scratch/stefan/7787277/working/3D/352' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497492.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497492.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497492/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497492 none C#CCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 147, 159, 56, 56, 56, 38, 38, 38, 38, 38, 36, 27, 36, 13, 1, 1, 1, 1, 1, 1, 1, 38, 201, 186, 188, 175, 175, 159, 159, 56, 38, 38, 38, 38, 38, 27, 27, 1, 38, 38] 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])
total number of confs: 937
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: REAL300025497492 none C#CCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [46, 46, 22, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 38, 38, 38, 38, 38, 1, 46, 43, 43, 28, 28, 17, 17, 5, 1, 1, 1, 1, 1, 5, 5, 38, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 277
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497492 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497492
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497492/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497492
Building REAL300025497493
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497493'
/scratch/stefan/7787277/working/building/REAL300025497493 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497493

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497493/0 /scratch/stefan/7787277/working/building/REAL300025497493 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 353)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/353
`/scratch/stefan/7787277/working/3D/353' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(Cl)OC=C2)C1)

`REAL300025497493.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497493.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497493/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497493 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(Cl)OC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 16, 12, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 14, 24, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 1, 14, 14, 73, 1, 1, 1, 1, 1, 5, 14, 14, 1, 1] 201
rigid atoms, others: [32, 1, 36, 37, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35])
total number of confs: 160
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497493 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(Cl)OC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 16, 12, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 14, 32, 70, 100, 201, 201, 201, 201, 201, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 14, 70, 70, 201, 14, 14, 14, 14, 14, 5, 1, 1, 14, 14] 201
rigid atoms, others: [34, 35, 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, 36, 37])
total number of confs: 486
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497493 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(Cl)OC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 16, 12, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 41, 13, 1, 1, 1, 1, 1, 1, 1, 54, 73, 73, 73, 73, 73, 93, 93, 93, 201, 201, 201, 201, 201, 73, 41, 41, 1, 73, 73, 73, 73, 73, 93, 201, 201, 73, 73] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 461
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497493 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497493
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497493/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497493
Building REAL300025497494
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497494'
/scratch/stefan/7787277/working/building/REAL300025497494 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497494

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497494/0 /scratch/stefan/7787277/working/building/REAL300025497494 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 354)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/354
`/scratch/stefan/7787277/working/3D/354' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NS1)

`REAL300025497494.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497494.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497494/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497494 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 36, 62, 143, 143, 143, 143, 143, 1, 10, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 37, 37, 143, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 6, 7, 8, 9, 10, 11, 12, 22, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 312
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497494 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 201, 201, 201, 201, 201, 143, 143, 143, 143, 143, 105, 44, 105, 13, 1, 1, 1, 1, 1, 1, 1, 143, 201, 201, 201, 201, 201, 201, 201, 143, 143, 143, 143, 143, 44, 44, 1, 143, 143] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 603
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497494 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 14, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 31, 31, 87, 124, 201, 201, 201, 201, 201, 10, 1, 1, 2, 2, 2, 1, 3, 10, 10, 10, 10, 10, 87, 87, 201, 10, 10] 201
rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 523
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497494 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497494
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497494/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497494
Building REAL300025497495
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497495'
/scratch/stefan/7787277/working/building/REAL300025497495 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497495

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497495/0 /scratch/stefan/7787277/working/building/REAL300025497495 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 355)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/355
`/scratch/stefan/7787277/working/3D/355' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497495.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497495.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497495/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497495 none CCN1C=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 9, 9, 9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 38, 111, 111, 111, 111, 111, 1, 17, 17, 17, 17, 17, 9, 9, 5, 1, 1, 1, 1, 1, 21, 21, 111, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 269
number of broken/clashed sets: 46
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497495 none CCN1C=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 137, 137, 137, 137, 137, 135, 135, 135, 111, 111, 111, 111, 111, 69, 29, 69, 13, 1, 1, 1, 1, 1, 1, 1, 111, 201, 201, 201, 201, 201, 137, 137, 135, 111, 111, 111, 111, 111, 29, 29, 1, 111, 111] 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])
total number of confs: 764
number of broken/clashed sets: 46
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497495 none CCN1C=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 8, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 9, 9, 9, 9, 9, 24, 24, 50, 73, 137, 137, 137, 137, 137, 9, 4, 4, 4, 4, 4, 1, 1, 4, 9, 9, 9, 9, 9, 50, 50, 137, 9, 9] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 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, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 345
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497495 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497495
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497495/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497495
Building REAL300025497496
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497496'
/scratch/stefan/7787277/working/building/REAL300025497496 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497496

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497496/0 /scratch/stefan/7787277/working/building/REAL300025497496 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 356)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/356
`/scratch/stefan/7787277/working/3D/356' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCOCC2)C1)

`REAL300025497496.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497496.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497496/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497496 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCOCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 1, 4, 4, 4, 21, 21, 21, 21, 21, 21, 1, 13, 13, 77, 1, 1, 1, 1, 1, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1] 201
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 14, 15, 46, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 184
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497496 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCOCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 40, 78, 115, 201, 201, 201, 201, 201, 21, 21, 21, 21, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 21, 78, 78, 201, 21, 21, 21, 21, 21, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 201
rigid atoms, others: [35, 36, 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, 46, 47])
total number of confs: 506
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497496 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCOCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 34, 12, 1, 1, 1, 1, 1, 1, 1, 60, 77, 77, 77, 77, 77, 117, 117, 117, 201, 201, 201, 201, 201, 201, 77, 34, 34, 1, 77, 77, 77, 77, 77, 117, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77] 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: 642
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497496 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497496
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497496/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497496
Building REAL300025497497
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497497'
/scratch/stefan/7787277/working/building/REAL300025497497 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497497

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497497/0 /scratch/stefan/7787277/working/building/REAL300025497497 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 357)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/357
`/scratch/stefan/7787277/working/3D/357' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=NC=CN1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497497.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497497.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497497/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497497 none O=C(CCC1=NC=CN1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 41, 143, 143, 143, 143, 143, 1, 12, 12, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 22, 22, 143, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 288
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497497 none O=C(CCC1=NC=CN1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [180, 180, 180, 201, 201, 201, 201, 201, 201, 143, 143, 143, 143, 143, 78, 30, 78, 13, 1, 1, 1, 1, 1, 1, 1, 143, 201, 201, 201, 201, 201, 201, 201, 180, 143, 143, 143, 143, 143, 30, 30, 1, 143, 143] 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])
total number of confs: 602
number of broken/clashed sets: 53
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497497 none O=C(CCC1=NC=CN1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 5, 5, 1, 1, 1, 1, 1, 1, 10, 10, 23, 23, 23, 23, 23, 40, 40, 75, 112, 201, 201, 201, 201, 201, 23, 5, 5, 5, 5, 1, 1, 1, 10, 23, 23, 23, 23, 23, 75, 75, 201, 23, 23] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 512
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497497 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497497
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497497/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497497
Building REAL300025497498
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497498'
/scratch/stefan/7787277/working/building/REAL300025497498 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497498

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497498/0 /scratch/stefan/7787277/working/building/REAL300025497498 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 358)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/358
`/scratch/stefan/7787277/working/3D/358' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC(O)CC2)C1)

`REAL300025497498.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497498.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497498/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497498 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC(O)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 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, 4, 7, 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, 19, 32, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 23, 23, 23, 23, 23, 1, 19, 19, 80, 1, 1, 1, 1, 1, 5, 23, 23, 23, 23, 23, 23, 69, 23, 23, 23, 23, 1, 1] 603
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 14, 15, 46, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 285
number of broken/clashed sets: 51
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497498 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC(O)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 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, 4, 7, 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: [51, 23, 51, 98, 139, 201, 201, 201, 201, 201, 23, 23, 23, 23, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 23, 98, 98, 201, 23, 23, 23, 23, 23, 6, 1, 1, 1, 1, 1, 1, 3, 1, 1, 1, 1, 23, 23] 603
rigid atoms, others: [35, 36, 37, 38, 39, 40, 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, 41, 46, 47])
total number of confs: 562
number of broken/clashed sets: 51
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497498 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC(O)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 7, 7, 7, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [70, 44, 13, 1, 1, 1, 1, 1, 1, 1, 70, 80, 80, 80, 80, 80, 104, 104, 104, 201, 201, 201, 201, 201, 201, 80, 44, 44, 1, 80, 80, 80, 80, 80, 104, 201, 201, 201, 201, 201, 201, 603, 201, 201, 201, 201, 80, 80] 603
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 1263
number of broken/clashed sets: 51
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497498 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497498
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497498/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497498
Building REAL300025497499
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497499'
/scratch/stefan/7787277/working/building/REAL300025497499 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497499

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497499/0 /scratch/stefan/7787277/working/building/REAL300025497499 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 359)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/359
`/scratch/stefan/7787277/working/3D/359' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497499.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497499.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497499/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497499 none CC(C)(O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [186, 193, 201, 201, 113, 113, 113, 69, 69, 69, 69, 69, 54, 41, 54, 13, 1, 1, 1, 1, 1, 1, 1, 69, 201, 201, 201, 201, 201, 201, 603, 193, 193, 113, 69, 69, 69, 69, 69, 41, 41, 1, 69, 69] 603
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])
total number of confs: 1477
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: REAL300025497499 none CC(C)(O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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, 19, 23, 24, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 20, 69, 69, 69, 69, 69, 1, 24, 24, 24, 24, 24, 24, 72, 19, 19, 5, 1, 1, 1, 1, 1, 11, 11, 69, 1, 1] 603
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 304
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497499 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497499
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497499/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497499
Building REAL300025497500
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497500'
/scratch/stefan/7787277/working/building/REAL300025497500 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497500

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497500/0 /scratch/stefan/7787277/working/building/REAL300025497500 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 360)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/360
`/scratch/stefan/7787277/working/3D/360' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025497500.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497500.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497500/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497500 none CC1=CC=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [14, 14, 9, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 33, 83, 83, 83, 83, 83, 1, 14, 14, 14, 14, 9, 14, 5, 1, 1, 1, 1, 1, 19, 19, 83, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 209
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497500 none CC1=CC=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 108, 108, 108, 83, 83, 83, 83, 83, 67, 36, 67, 13, 1, 1, 1, 1, 1, 1, 1, 83, 201, 201, 201, 201, 201, 201, 108, 83, 83, 83, 83, 83, 36, 36, 1, 83, 83] 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])
total number of confs: 536
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497500 none CC1=CC=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 14, 37, 37, 80, 118, 201, 201, 201, 201, 201, 14, 1, 2, 2, 2, 1, 1, 4, 14, 14, 14, 14, 14, 80, 80, 201, 14, 14] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 528
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497500 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497500
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497500/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497500
Building REAL300025497501
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497501'
/scratch/stefan/7787277/working/building/REAL300025497501 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497501

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497501/0 /scratch/stefan/7787277/working/building/REAL300025497501 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 361)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/361
`/scratch/stefan/7787277/working/3D/361' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1)

`REAL300025497501.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497501.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497501/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497501 none COC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [165, 165, 88, 88, 88, 48, 48, 48, 48, 48, 48, 43, 48, 13, 1, 1, 1, 1, 1, 1, 1, 48, 165, 201, 201, 165, 165, 165, 165, 88, 48, 48, 48, 48, 48, 43, 43, 1, 48, 48, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 770
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497501 none COC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 1, 8, 24, 24, 24, 52, 52, 52, 52, 52, 78, 78, 109, 134, 201, 201, 201, 201, 201, 52, 1, 1, 1, 14, 14, 14, 8, 24, 52, 52, 52, 52, 52, 109, 109, 201, 52, 52, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 40, 41, 42, 43, 44, 22, 23, 24] set([0, 1, 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])
total number of confs: 592
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497501 none COC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 29, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 12, 48, 48, 48, 48, 48, 1, 29, 52, 52, 37, 37, 37, 29, 6, 1, 1, 1, 1, 1, 8, 8, 48, 1, 1, 52, 52, 52, 52, 52] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 21, 39, 38, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44])
total number of confs: 259
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497501 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497501
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497501/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497501
Building REAL300025497502
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497502'
/scratch/stefan/7787277/working/building/REAL300025497502 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497502

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497502/0 /scratch/stefan/7787277/working/building/REAL300025497502 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 362)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/362
`/scratch/stefan/7787277/working/3D/362' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1)

`REAL300025497502.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497502.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497502/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497502 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 26, 106, 106, 106, 106, 106, 1, 12, 13, 13, 29, 29, 29, 29, 29, 4, 1, 1, 1, 1, 1, 13, 13, 106, 1, 1, 13, 13] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43])
total number of confs: 266
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497502 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 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
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, 142, 142, 142, 106, 106, 106, 106, 106, 78, 30, 78, 13, 1, 1, 1, 1, 1, 1, 1, 106, 192, 192, 192, 201, 201, 201, 201, 201, 142, 106, 106, 106, 106, 106, 30, 30, 1, 106, 106, 192, 192] 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: 568
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497502 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 6, 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
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, 5, 13, 13, 13, 13, 13, 23, 23, 54, 91, 192, 192, 192, 192, 192, 13, 1, 1, 1, 5, 5, 5, 4, 4, 5, 13, 13, 13, 13, 13, 54, 54, 192, 13, 13, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 42, 43, 23, 24, 25] set([0, 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: 449
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497502 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497502
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497502/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497502
Building REAL300025497503
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497503'
/scratch/stefan/7787277/working/building/REAL300025497503 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497503

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497503/0 /scratch/stefan/7787277/working/building/REAL300025497503 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 363)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/363
`/scratch/stefan/7787277/working/3D/363' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497503.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497503.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497503/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497503 none CN1N=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 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, 6, 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: [12, 12, 12, 12, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 48, 143, 143, 143, 143, 143, 1, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 17, 17, 143, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 39, 8, 9, 10, 11, 12, 13, 14, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 256
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497503 none CN1N=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 200, 200, 200, 143, 143, 143, 143, 143, 117, 49, 117, 13, 1, 1, 1, 1, 1, 1, 1, 143, 201, 201, 201, 201, 200, 143, 143, 143, 143, 143, 49, 49, 1, 143, 143] 201
rigid atoms, others: [37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 603
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497503 none CN1N=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 24, 24, 60, 108, 201, 201, 201, 201, 201, 12, 2, 2, 2, 1, 5, 12, 12, 12, 12, 12, 60, 60, 201, 12, 12] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 461
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497503 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497503
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497503/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497503
Building REAL300025497504
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497504'
/scratch/stefan/7787277/working/building/REAL300025497504 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497504

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497504/0 /scratch/stefan/7787277/working/building/REAL300025497504 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 364)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/364
`/scratch/stefan/7787277/working/3D/364' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497504.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497504.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497504/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497504 none CCCCC(C)C(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 98, 176, 98, 98, 53, 53, 53, 53, 53, 46, 29, 46, 13, 1, 1, 1, 1, 1, 1, 1, 53, 201, 201, 201, 201, 201, 201, 201, 201, 201, 176, 176, 176, 176, 98, 53, 53, 53, 53, 53, 29, 29, 1, 53, 53] 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])
total number of confs: 826
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: REAL300025497504 none CCCCC(C)C(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 5, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 53, 53, 53, 53, 53, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 6, 6, 53, 1, 1] 201
rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 220
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497504 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497504
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497504/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497504
Building REAL300025497505
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497505'
/scratch/stefan/7787277/working/building/REAL300025497505 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497505

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497505/0 /scratch/stefan/7787277/working/building/REAL300025497505 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 365)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/365
`/scratch/stefan/7787277/working/3D/365' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1)

`REAL300025497505.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497505.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497505/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497505 none CC1CC(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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]
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: [10, 10, 10, 10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 58, 160, 160, 160, 160, 160, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 1, 29, 29, 160, 1, 1] 190
rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 40, 46, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 316
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497505 none CC1CC(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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]
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: [190, 190, 190, 190, 190, 179, 179, 179, 160, 160, 160, 160, 160, 123, 45, 123, 13, 1, 1, 1, 1, 1, 1, 1, 160, 190, 190, 190, 190, 190, 190, 190, 190, 190, 190, 190, 190, 179, 160, 160, 160, 160, 160, 45, 45, 1, 160, 160] 190
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: 557
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497505 none CC1CC(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
190  conformations in input
total number of sets (complete confs): 190
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 32, 32, 84, 116, 190, 190, 190, 190, 190, 10, 1, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 1, 4, 10, 10, 10, 10, 10, 84, 84, 190, 10, 10] 190
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 25, 36, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 508
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497505 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497505
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497505/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497505
Building REAL300025497506
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497506'
/scratch/stefan/7787277/working/building/REAL300025497506 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497506

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497506/0 /scratch/stefan/7787277/working/building/REAL300025497506 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 366)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/366
`/scratch/stefan/7787277/working/3D/366' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2C[C@@H]2C(F)F)C1)

`REAL300025497506.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497506.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497506/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497506 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2C[C@@H]2C(F)F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', '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, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 16, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 1, 4, 4, 4, 24, 24, 24, 24, 24, 44, 44, 1, 10, 10, 61, 1, 1, 1, 1, 1, 4, 24, 24, 44, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 10, 11, 12, 13, 14, 15, 39, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38])
total number of confs: 259
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497506 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2C[C@@H]2C(F)F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', '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, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 50, 79, 111, 201, 201, 201, 201, 201, 24, 24, 24, 24, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 24, 79, 79, 201, 24, 24, 24, 24, 24, 11, 1, 1, 8, 24, 24] 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: 525
number of broken/clashed sets: 34
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497506 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2C[C@@H]2C(F)F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', '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, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 27, 12, 1, 1, 1, 1, 1, 1, 1, 47, 61, 61, 61, 61, 61, 94, 94, 94, 201, 201, 201, 201, 201, 201, 201, 61, 27, 27, 1, 61, 61, 61, 61, 61, 94, 201, 201, 201, 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])
total number of confs: 609
number of broken/clashed sets: 34
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497506 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497506
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497506/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497506
Building REAL300025497507
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497507'
/scratch/stefan/7787277/working/building/REAL300025497507 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497507

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497507/0 /scratch/stefan/7787277/working/building/REAL300025497507 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 367)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/367
`/scratch/stefan/7787277/working/3D/367' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=COC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497507.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497507.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497507/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497507 none CC1=COC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 20, 77, 77, 77, 77, 77, 1, 18, 18, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 12, 12, 77, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497507 none CC1=COC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 98, 98, 98, 77, 77, 77, 77, 77, 65, 41, 65, 13, 1, 1, 1, 1, 1, 1, 1, 77, 201, 201, 201, 201, 201, 201, 201, 98, 77, 77, 77, 77, 77, 41, 41, 1, 77, 77] 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])
total number of confs: 478
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497507 none CC1=COC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 18, 18, 18, 18, 18, 37, 37, 76, 107, 201, 201, 201, 201, 201, 18, 2, 2, 2, 1, 2, 2, 2, 7, 18, 18, 18, 18, 18, 76, 76, 201, 18, 18] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 542
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497507 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497507
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497507/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497507
Building REAL300025497508
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497508'
/scratch/stefan/7787277/working/building/REAL300025497508 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497508

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497508/0 /scratch/stefan/7787277/working/building/REAL300025497508 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 368)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/368
`/scratch/stefan/7787277/working/3D/368' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497508.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497508.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497508/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497508 none CC1(C)CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 25, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 31, 69, 69, 69, 69, 69, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 5, 1, 1, 1, 1, 1, 18, 18, 69, 1, 1, 25, 25] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46])
total number of confs: 209
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497508 none CC1(C)CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 83, 83, 83, 69, 69, 69, 69, 69, 59, 37, 59, 13, 1, 1, 1, 1, 1, 1, 1, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 69, 69, 69, 69, 69, 37, 37, 1, 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])
total number of confs: 641
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497508 none CC1(C)CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 1, 9, 9, 9, 25, 25, 25, 25, 25, 52, 52, 93, 134, 201, 201, 201, 201, 201, 25, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 9, 25, 25, 25, 25, 25, 93, 93, 201, 25, 25, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 46, 24, 33, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 564
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497508 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497508
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497508/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497508
Building REAL300025497509
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497509'
/scratch/stefan/7787277/working/building/REAL300025497509 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497509

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497509/0 /scratch/stefan/7787277/working/building/REAL300025497509 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 369)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/369
`/scratch/stefan/7787277/working/3D/369' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[C@@H](O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497509.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497509.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497509/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497509 none CC(C)[C@@H](O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
1  hydrogens need rotated
603  conformations in input
total number of sets (complete confs): 603
using faster count positions algorithm for large data
unique positions, atoms: [201, 191, 201, 153, 191, 191, 153, 153, 90, 90, 90, 90, 90, 75, 50, 75, 13, 1, 1, 1, 1, 1, 1, 1, 90, 201, 201, 201, 201, 201, 201, 201, 573, 153, 90, 90, 90, 90, 90, 50, 50, 1, 90, 90] 603
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43])
total number of confs: 1321
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: REAL300025497509 none CC(C)[C@@H](O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 7, 12, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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, 6, 7, 7, 7, 7, 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: [27, 17, 27, 5, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 19, 90, 90, 90, 90, 90, 1, 27, 27, 27, 27, 27, 27, 27, 51, 5, 1, 1, 1, 1, 1, 11, 11, 90, 1, 1] 603
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 293
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497509 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497509
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497509/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497509
Building REAL300025497510
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497510'
/scratch/stefan/7787277/working/building/REAL300025497510 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497510

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497510/0 /scratch/stefan/7787277/working/building/REAL300025497510 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 370)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/370
`/scratch/stefan/7787277/working/3D/370' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497510.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497510.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497510/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497510 none CCOC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [34, 34, 20, 20, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 29, 110, 110, 110, 110, 110, 1, 20, 34, 34, 34, 34, 34, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 17, 17, 110, 1, 1, 20, 20] 201
rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47])
total number of confs: 264
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497510 none CCOC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 138, 138, 138, 110, 110, 110, 110, 110, 92, 42, 92, 13, 1, 1, 1, 1, 1, 1, 1, 110, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 138, 110, 110, 110, 110, 110, 42, 42, 1, 110, 110, 201, 201] 201
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 647
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497510 none CCOC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 20, 20, 51, 51, 78, 113, 201, 201, 201, 201, 201, 20, 1, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 20, 20, 20, 20, 20, 78, 78, 201, 20, 20, 1, 1] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 34, 46, 47, 25, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 481
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497510 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497510
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497510/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497510
Building REAL300025497511
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497511'
/scratch/stefan/7787277/working/building/REAL300025497511 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497511

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497511/0 /scratch/stefan/7787277/working/building/REAL300025497511 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 371)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/371
`/scratch/stefan/7787277/working/3D/371' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1)

`REAL300025497511.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497511.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497511/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497511 none CC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 24, 86, 86, 86, 86, 86, 1, 21, 21, 21, 21, 21, 21, 21, 14, 14, 5, 1, 1, 1, 1, 1, 12, 12, 86, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 41] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 218
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497511 none CC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens need 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, 112, 112, 112, 86, 86, 86, 86, 86, 55, 30, 55, 13, 1, 1, 1, 1, 1, 1, 1, 86, 201, 201, 201, 201, 201, 201, 201, 156, 156, 112, 86, 86, 86, 86, 86, 30, 30, 1, 86, 86, 201, 201, 201, 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, 48, 49])
total number of confs: 767
number of broken/clashed sets: 45
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497511 none CC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens need rotated
201  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, 8, 8, 8, 21, 21, 21, 21, 21, 41, 41, 75, 119, 201, 201, 201, 201, 201, 21, 1, 1, 1, 1, 2, 2, 2, 5, 5, 8, 21, 21, 21, 21, 21, 75, 75, 201, 21, 21, 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: 526
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497511 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497511
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497511/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497511
Building REAL300025497512
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497512'
/scratch/stefan/7787277/working/building/REAL300025497512 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497512

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497512/0 /scratch/stefan/7787277/working/building/REAL300025497512 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 372)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/372
`/scratch/stefan/7787277/working/3D/372' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1)

`REAL300025497512.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497512.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497512/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497512 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 43, 111, 111, 111, 111, 111, 1, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 24, 24, 111, 1, 1] 155
rigid atoms, others: [32, 33, 34, 38, 6, 7, 8, 9, 10, 11, 12, 22, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 243
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497512 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [155, 155, 155, 141, 141, 141, 111, 111, 111, 111, 111, 90, 41, 90, 13, 1, 1, 1, 1, 1, 1, 1, 111, 155, 155, 155, 155, 155, 155, 141, 111, 111, 111, 111, 111, 41, 41, 1, 111, 111] 155
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 472
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497512 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
155  conformations in input
total number of sets (complete confs): 155
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 40, 40, 77, 100, 155, 155, 155, 155, 155, 16, 1, 1, 2, 2, 2, 1, 6, 16, 16, 16, 16, 16, 77, 77, 155, 16, 16] 155
rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 421
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497512 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497512
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497512/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497512
Building REAL300025497513
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497513'
/scratch/stefan/7787277/working/building/REAL300025497513 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497513

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497513/0 /scratch/stefan/7787277/working/building/REAL300025497513 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 373)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/373
`/scratch/stefan/7787277/working/3D/373' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1)

`REAL300025497513.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497513.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497513/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497513 none CC1=NN=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens 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, 21, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 12, 66, 66, 66, 66, 66, 1, 36, 36, 36, 36, 21, 21, 4, 1, 1, 1, 1, 1, 7, 7, 66, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 192
number of broken/clashed sets: 75
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497513 none CC1=NN=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations 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, 99, 99, 99, 66, 66, 66, 66, 66, 50, 31, 50, 13, 1, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 201, 195, 195, 99, 66, 66, 66, 66, 66, 31, 31, 1, 66, 66] 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])
total number of confs: 787
number of broken/clashed sets: 75
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497513 none CC1=NN=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
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, 23, 23, 23, 36, 36, 36, 36, 36, 50, 50, 88, 132, 201, 201, 201, 201, 201, 36, 1, 2, 2, 2, 7, 7, 23, 36, 36, 36, 36, 36, 88, 88, 201, 36, 36] 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: 566
number of broken/clashed sets: 75
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497513 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497513
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497513/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497513
Building REAL300025497514
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497514'
/scratch/stefan/7787277/working/building/REAL300025497514 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497514

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497514/0 /scratch/stefan/7787277/working/building/REAL300025497514 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 374)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/374
`/scratch/stefan/7787277/working/3D/374' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025497514.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497514.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497514/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497514 none CN1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 6, 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, 6, 7, 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: [12, 12, 12, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 46, 111, 111, 111, 111, 111, 1, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 25, 25, 111, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 7, 8, 9, 10, 11, 12, 13, 23, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497514 none CN1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 142, 142, 142, 111, 111, 111, 111, 111, 85, 38, 85, 13, 1, 1, 1, 1, 1, 1, 1, 111, 201, 201, 201, 201, 201, 142, 111, 111, 111, 111, 111, 38, 38, 1, 111, 111] 201
rigid atoms, others: [37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 563
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497514 none CN1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 37, 37, 89, 129, 201, 201, 201, 201, 201, 12, 1, 2, 2, 2, 1, 5, 12, 12, 12, 12, 12, 89, 89, 201, 12, 12] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 551
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497514 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497514
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497514/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497514
Building REAL300025497515
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497515'
/scratch/stefan/7787277/working/building/REAL300025497515 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497515

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497515/0 /scratch/stefan/7787277/working/building/REAL300025497515 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 375)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/375
`/scratch/stefan/7787277/working/3D/375' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)NCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497515.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497515.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497515/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497515 none CNC(=O)NCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [200, 200, 200, 200, 200, 176, 93, 93, 93, 73, 73, 73, 73, 73, 51, 29, 51, 13, 1, 1, 1, 1, 1, 1, 1, 73, 200, 200, 200, 200, 200, 200, 200, 176, 176, 93, 73, 73, 73, 73, 73, 29, 29, 1, 73, 73] 200
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])
total number of confs: 826
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497515 none CNC(=O)NCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [30, 26, 26, 26, 25, 19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 16, 73, 73, 73, 73, 73, 1, 30, 30, 30, 30, 26, 25, 25, 19, 19, 5, 1, 1, 1, 1, 1, 8, 8, 73, 1, 1] 200
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 226
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497515 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497515
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497515/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497515
Building REAL300025497516
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497516'
/scratch/stefan/7787277/working/building/REAL300025497516 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497516

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497516/0 /scratch/stefan/7787277/working/building/REAL300025497516 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 376)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/376
`/scratch/stefan/7787277/working/3D/376' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(F)C=CS2)C1)

`REAL300025497516.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497516.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497516/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497516 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(F)C=CS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 15, 1, 1, 14, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 14, 30, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 14, 14, 80, 1, 1, 1, 1, 1, 5, 15, 15, 1, 1] 201
rigid atoms, others: [32, 1, 36, 37, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35])
total number of confs: 172
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497516 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(F)C=CS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 15, 1, 1, 14, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 15, 34, 66, 100, 201, 201, 201, 201, 201, 15, 15, 15, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 66, 66, 201, 15, 15, 15, 15, 15, 7, 1, 1, 15, 15] 201
rigid atoms, others: [34, 35, 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, 36, 37])
total number of confs: 465
number of broken/clashed sets: 24
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497516 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(F)C=CS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'F', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 15, 1, 1, 14, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 35, 13, 1, 1, 1, 1, 1, 1, 1, 59, 80, 80, 80, 80, 80, 113, 113, 113, 201, 201, 201, 201, 201, 80, 35, 35, 1, 80, 80, 80, 80, 80, 113, 201, 201, 80, 80] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 541
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497516 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497516
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497516/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497516
Building REAL300025497517
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497517'
/scratch/stefan/7787277/working/building/REAL300025497517 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497517

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497517/0 /scratch/stefan/7787277/working/building/REAL300025497517 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 377)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/377
`/scratch/stefan/7787277/working/3D/377' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025497517.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497517.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497517/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497517 none CCN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 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, 6, 6, 6, 6, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 35, 96, 96, 96, 96, 96, 1, 6, 17, 17, 17, 17, 17, 6, 5, 1, 1, 1, 1, 1, 19, 19, 96, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 241
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497517 none CCN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 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, 124, 124, 124, 124, 124, 124, 124, 96, 96, 96, 96, 96, 77, 39, 77, 13, 1, 1, 1, 1, 1, 1, 1, 96, 124, 201, 201, 201, 201, 201, 124, 124, 96, 96, 96, 96, 96, 39, 39, 1, 96, 96] 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])
total number of confs: 861
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497517 none CCN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 18, 18, 42, 66, 124, 124, 124, 124, 124, 6, 1, 8, 8, 8, 7, 7, 1, 3, 6, 6, 6, 6, 6, 42, 42, 124, 6, 6] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 318
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497517 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497517
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497517/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497517
Building REAL300025497518
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497518'
/scratch/stefan/7787277/working/building/REAL300025497518 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497518

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497518/0 /scratch/stefan/7787277/working/building/REAL300025497518 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 378)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/378
`/scratch/stefan/7787277/working/3D/378' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1)

`REAL300025497518.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497518.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497518/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497518 none CC(C)(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 96, 139, 69, 69, 69, 52, 52, 52, 52, 52, 46, 26, 46, 12, 1, 1, 1, 1, 1, 1, 1, 52, 139, 201, 201, 139, 139, 139, 139, 139, 139, 96, 96, 69, 52, 52, 52, 52, 52, 26, 26, 1, 52, 52, 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])
total number of confs: 826
number of broken/clashed sets: 65
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497518 none CC(C)(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 13, 13, 13, 19, 19, 19, 19, 19, 29, 29, 63, 112, 201, 201, 201, 201, 201, 19, 1, 1, 1, 6, 6, 6, 6, 6, 6, 8, 8, 13, 19, 19, 19, 19, 19, 63, 63, 201, 19, 19, 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: 500
number of broken/clashed sets: 65
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497518 none CC(C)(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 7, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 15, 52, 52, 52, 52, 52, 1, 11, 19, 19, 11, 11, 11, 11, 11, 11, 7, 7, 5, 1, 1, 1, 1, 1, 7, 7, 52, 1, 1, 19, 19, 19, 19, 19] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 43, 22, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46, 47, 48, 49])
total number of confs: 154
number of broken/clashed sets: 65
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497518 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497518
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497518/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497518
Building REAL300025497519
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497519'
/scratch/stefan/7787277/working/building/REAL300025497519 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497519

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497519/0 /scratch/stefan/7787277/working/building/REAL300025497519 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 379)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/379
`/scratch/stefan/7787277/working/3D/379' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1N=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497519.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497519.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497519/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497519 none CCN1N=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 14, 14, 14, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 30, 95, 95, 95, 95, 95, 1, 27, 27, 27, 27, 27, 14, 4, 1, 1, 1, 1, 1, 17, 17, 95, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 251
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497519 none CCN1N=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 141, 120, 120, 120, 95, 95, 95, 95, 95, 60, 28, 60, 13, 1, 1, 1, 1, 1, 1, 1, 95, 201, 201, 201, 201, 201, 141, 120, 95, 95, 95, 95, 95, 28, 28, 1, 95, 95] 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])
total number of confs: 737
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497519 none CCN1N=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 8, 8, 8, 14, 14, 14, 14, 14, 29, 29, 52, 80, 141, 141, 141, 141, 141, 14, 6, 6, 6, 6, 6, 1, 8, 14, 14, 14, 14, 14, 52, 52, 141, 14, 14] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 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, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 356
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497519 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497519
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497519/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497519
Building REAL300025497520
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497520'
/scratch/stefan/7787277/working/building/REAL300025497520 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497520

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497520/0 /scratch/stefan/7787277/working/building/REAL300025497520 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 380)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/380
`/scratch/stefan/7787277/working/3D/380' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CSC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497520.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497520.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497520/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497520 none CC1=CSC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 6, 6, 22, 44, 117, 117, 117, 117, 117, 1, 20, 20, 20, 20, 20, 6, 1, 1, 1, 1, 1, 22, 22, 117, 1, 1, 20] 201
rigid atoms, others: [32, 33, 34, 38, 7, 8, 9, 10, 11, 12, 13, 23, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40])
total number of confs: 253
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497520 none CC1=CSC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 169, 169, 169, 117, 117, 117, 117, 117, 94, 43, 94, 13, 1, 1, 1, 1, 1, 1, 1, 117, 201, 201, 201, 201, 201, 169, 117, 117, 117, 117, 117, 43, 43, 1, 117, 117, 201] 201
rigid atoms, others: [37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 599
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497520 none CC1=CSC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 14, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 20, 20, 20, 20, 20, 52, 52, 99, 133, 201, 201, 201, 201, 201, 20, 1, 2, 2, 2, 1, 7, 20, 20, 20, 20, 20, 99, 99, 201, 20, 20, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 24, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 552
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497520 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497520
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497520/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497520
Building REAL300025497521
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497521'
/scratch/stefan/7787277/working/building/REAL300025497521 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497521

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497521/0 /scratch/stefan/7787277/working/building/REAL300025497521 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 381)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/381
`/scratch/stefan/7787277/working/3D/381' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC2(F)F)C1)

`REAL300025497521.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497521.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497521/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497521 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC2(F)F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 1, 4, 4, 4, 22, 22, 22, 22, 1, 13, 13, 82, 1, 1, 1, 1, 1, 4, 22, 22, 22, 1, 1] 201
rigid atoms, others: [1, 36, 37, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34, 35])
total number of confs: 189
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497521 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC2(F)F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 22, 47, 90, 119, 201, 201, 201, 201, 201, 22, 22, 22, 22, 10, 10, 1, 10, 1, 1, 1, 1, 1, 22, 90, 90, 201, 22, 22, 22, 22, 22, 10, 1, 1, 1, 22, 22] 201
rigid atoms, others: [33, 34, 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, 36, 37])
total number of confs: 549
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497521 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC2(F)F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 39, 13, 1, 1, 1, 1, 1, 1, 1, 63, 82, 82, 82, 82, 82, 106, 106, 106, 201, 201, 201, 201, 82, 39, 39, 1, 82, 82, 82, 82, 82, 106, 201, 201, 201, 82, 82] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 619
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497521 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497521
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497521/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497521
Building REAL300025497522
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497522'
/scratch/stefan/7787277/working/building/REAL300025497522 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497522

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497522/0 /scratch/stefan/7787277/working/building/REAL300025497522 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 382)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/382
`/scratch/stefan/7787277/working/3D/382' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)=CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497522.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497522.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497522/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497522 none CCC(C)=CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 5, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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, 108, 108, 108, 66, 66, 66, 54, 54, 54, 54, 54, 32, 21, 32, 11, 1, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 201, 108, 108, 108, 108, 66, 54, 54, 54, 54, 54, 21, 21, 1, 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])
total number of confs: 909
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: REAL300025497522 none CCC(C)=CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 5, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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: [25, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 12, 20, 54, 54, 54, 54, 54, 1, 25, 25, 25, 25, 25, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 12, 12, 54, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 209
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497522 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497522
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497522/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497522
Building REAL300025497523
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497523'
/scratch/stefan/7787277/working/building/REAL300025497523 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497523

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497523/0 /scratch/stefan/7787277/working/building/REAL300025497523 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 383)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/383
`/scratch/stefan/7787277/working/3D/383' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497523.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497523.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497523/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497523 none CC1=CN=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 7, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 23, 88, 88, 88, 88, 88, 1, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 12, 12, 88, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 196
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497523 none CC1=CN=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  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, 201, 201, 113, 113, 113, 88, 88, 88, 88, 88, 74, 39, 74, 13, 1, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 201, 201, 201, 113, 88, 88, 88, 88, 88, 39, 39, 1, 88, 88] 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])
total number of confs: 596
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497523 none CC1=CN=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 21, 21, 21, 21, 21, 52, 52, 88, 121, 201, 201, 201, 201, 201, 21, 2, 2, 2, 1, 1, 1, 9, 21, 21, 21, 21, 21, 88, 88, 201, 21, 21] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 537
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497523 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497523
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497523/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497523
Building REAL300025497524
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497524'
/scratch/stefan/7787277/working/building/REAL300025497524 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497524

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497524/0 /scratch/stefan/7787277/working/building/REAL300025497524 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 384)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/384
`/scratch/stefan/7787277/working/3D/384' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C#CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497524.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497524.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497524/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497524 none CC(C)C#CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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, 201, 201, 201, 162, 162, 162, 162, 162, 135, 56, 135, 13, 1, 1, 1, 1, 1, 1, 1, 162, 201, 201, 201, 201, 201, 201, 201, 201, 162, 162, 162, 162, 162, 56, 56, 1, 162, 162] 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])
total number of confs: 616
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497524 none CC(C)C#CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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: [6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 59, 162, 162, 162, 162, 162, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 22, 22, 162, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 297
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497524 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497524
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497524/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497524
Building REAL300025497525
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497525'
/scratch/stefan/7787277/working/building/REAL300025497525 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497525

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497525/0 /scratch/stefan/7787277/working/building/REAL300025497525 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 385)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/385
`/scratch/stefan/7787277/working/3D/385' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CS1)

`REAL300025497525.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497525.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497525/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497525 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 14, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 23, 83, 83, 83, 83, 83, 1, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 12, 12, 83, 1, 1, 20, 20] 201
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 37, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40])
total number of confs: 170
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497525 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 14, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 103, 103, 103, 83, 83, 83, 83, 83, 66, 42, 66, 13, 1, 1, 1, 1, 1, 1, 1, 83, 201, 201, 201, 201, 201, 201, 103, 83, 83, 83, 83, 83, 42, 42, 1, 83, 83, 201, 201] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 493
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497525 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 14, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 20, 20, 20, 20, 20, 38, 38, 73, 109, 201, 201, 201, 201, 201, 20, 1, 1, 1, 2, 2, 2, 9, 20, 20, 20, 20, 20, 73, 73, 201, 20, 20, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 39, 40, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 521
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497525 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497525
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497525/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497525
Building REAL300025497526
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497526'
/scratch/stefan/7787277/working/building/REAL300025497526 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497526

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497526/0 /scratch/stefan/7787277/working/building/REAL300025497526 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 386)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/386
`/scratch/stefan/7787277/working/3D/386' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1(O)CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497526.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497526.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497526/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497526 none O=C(CC1(O)CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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, 5, 5, 21, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 32, 104, 104, 104, 104, 104, 1, 21, 21, 75, 25, 25, 25, 25, 25, 25, 5, 1, 1, 1, 1, 1, 15, 15, 104, 1, 1] 603
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 334
number of broken/clashed sets: 180
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497526 none O=C(CC1(O)CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [134, 134, 134, 200, 201, 201, 201, 201, 104, 104, 104, 104, 104, 69, 30, 69, 13, 1, 1, 1, 1, 1, 1, 1, 104, 200, 200, 603, 201, 201, 201, 201, 201, 201, 134, 104, 104, 104, 104, 104, 30, 30, 1, 104, 104] 603
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])
total number of confs: 1318
number of broken/clashed sets: 180
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497526 none O=C(CC1(O)CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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, 4, 1, 1, 1, 1, 1, 1, 14, 14, 25, 25, 25, 25, 25, 45, 45, 86, 133, 201, 201, 201, 201, 201, 25, 4, 4, 6, 1, 1, 1, 1, 1, 1, 14, 25, 25, 25, 25, 25, 86, 86, 201, 25, 25] 603
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 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, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 557
number of broken/clashed sets: 180
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497526 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497526
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497526/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497526
Building REAL300025497527
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497527'
/scratch/stefan/7787277/working/building/REAL300025497527 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497527

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497527/0 /scratch/stefan/7787277/working/building/REAL300025497527 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 387)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/387
`/scratch/stefan/7787277/working/3D/387' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CNN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497527.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497527.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497527/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497527 none CC1=CNN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 56, 160, 160, 160, 160, 160, 1, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 19, 19, 160, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 279
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497527 none CC1=CNN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 160, 160, 160, 160, 160, 138, 53, 138, 13, 1, 1, 1, 1, 1, 1, 1, 160, 201, 201, 201, 201, 201, 201, 160, 160, 160, 160, 160, 53, 53, 1, 160, 160] 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])
total number of confs: 616
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497527 none CC1=CNN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 8, 8, 8, 8, 8, 22, 22, 57, 118, 201, 201, 201, 201, 201, 8, 2, 2, 2, 1, 1, 4, 8, 8, 8, 8, 8, 57, 57, 201, 8, 8] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 452
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497527 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497527
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497527/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497527
Building REAL300025497528
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497528'
/scratch/stefan/7787277/working/building/REAL300025497528 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497528

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497528/0 /scratch/stefan/7787277/working/building/REAL300025497528 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 388)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/388
`/scratch/stefan/7787277/working/3D/388' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CCC1)

`REAL300025497528.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497528.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497528/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497528 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 5, 5, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 113, 113, 113, 88, 88, 88, 88, 88, 70, 41, 70, 13, 1, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 201, 201, 201, 201, 113, 88, 88, 88, 88, 88, 41, 41, 1, 88, 88, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [36, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 640
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497528 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 5, 5, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  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, 8, 9, 26, 26, 26, 26, 26, 51, 51, 95, 136, 201, 201, 201, 201, 201, 26, 1, 1, 1, 1, 2, 2, 2, 9, 26, 26, 26, 26, 26, 95, 95, 201, 26, 26, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 39, 40, 41, 42, 43, 44, 21, 22, 23, 24] set([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])
total number of confs: 558
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497528 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)=C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 5, 5, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 34, 88, 88, 88, 88, 88, 1, 26, 26, 26, 26, 26, 26, 26, 5, 1, 1, 1, 1, 1, 19, 19, 88, 1, 1, 26, 26, 26, 26, 26, 26] 201
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 37, 20, 38, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40, 41, 42, 43, 44])
total number of confs: 235
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497528 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497528
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497528/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497528
Building REAL300025497529
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497529'
/scratch/stefan/7787277/working/building/REAL300025497529 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497529

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497529/0 /scratch/stefan/7787277/working/building/REAL300025497529 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 389)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/389
`/scratch/stefan/7787277/working/3D/389' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C#CC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497529.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497529.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497529/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497529 none O=C(C#CC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 58, 165, 165, 165, 165, 165, 1, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 22, 22, 165, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 7, 8, 9, 10, 11, 12, 13, 23, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 298
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497529 none O=C(C#CC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [201, 201, 201, 201, 201, 201, 201, 165, 165, 165, 165, 165, 133, 56, 133, 13, 1, 1, 1, 1, 1, 1, 1, 165, 201, 201, 201, 201, 201, 201, 165, 165, 165, 165, 165, 56, 56, 1, 165, 165] 201
rigid atoms, others: [37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 609
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497529 none O=C(C#CC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 1, 1, 5, 5, 5, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 19, 19, 48, 101, 201, 201, 201, 201, 201, 6, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 48, 48, 201, 6, 6] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29] set([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])
total number of confs: 418
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497529 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497529
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497529/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497529
Building REAL300025497530
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497530'
/scratch/stefan/7787277/working/building/REAL300025497530 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497530

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497530/0 /scratch/stefan/7787277/working/building/REAL300025497530 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 390)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/390
`/scratch/stefan/7787277/working/3D/390' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C#CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497530.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497530.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497530/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497530 none CC(C)(C)C#CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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, 201, 201, 201, 160, 160, 160, 160, 160, 132, 57, 132, 13, 1, 1, 1, 1, 1, 1, 1, 160, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 160, 160, 160, 160, 160, 57, 57, 1, 160, 160] 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])
total number of confs: 611
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: REAL300025497530 none CC(C)(C)C#CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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: [6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 58, 160, 160, 160, 160, 160, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 22, 22, 160, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 293
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497530 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497530
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497530/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497530
Building REAL300025497531
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497531'
/scratch/stefan/7787277/working/building/REAL300025497531 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497531

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497531/0 /scratch/stefan/7787277/working/building/REAL300025497531 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 391)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/391
`/scratch/stefan/7787277/working/3D/391' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N1)

`REAL300025497531.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497531.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497531/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497531 none CC1=NN=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [25, 25, 25, 25, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 32, 109, 109, 109, 109, 109, 1, 25, 25, 25, 25, 20, 20, 5, 1, 1, 1, 1, 1, 19, 19, 109, 1, 1, 25] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42])
total number of confs: 272
number of broken/clashed sets: 73
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497531 none CC1=NN=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 137, 137, 137, 109, 109, 109, 109, 109, 49, 28, 49, 13, 1, 1, 1, 1, 1, 1, 1, 109, 201, 201, 201, 201, 201, 201, 137, 109, 109, 109, 109, 109, 28, 28, 1, 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])
total number of confs: 704
number of broken/clashed sets: 73
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497531 none CC1=NN=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 25, 25, 25, 25, 25, 43, 43, 81, 118, 201, 201, 201, 201, 201, 25, 1, 2, 2, 2, 5, 5, 14, 25, 25, 25, 25, 25, 81, 81, 201, 25, 25, 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: 543
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497531 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497531/1 /scratch/stefan/7787277/working/building/REAL300025497531 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 392)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/392
`/scratch/stefan/7787277/working/3D/392' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1)

`REAL300025497531.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497531.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497531/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497531 none CC1=NC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 10, 51, 51, 51, 51, 51, 1, 40, 40, 40, 40, 40, 15, 15, 4, 1, 1, 1, 1, 1, 6, 6, 51, 1, 1, 40] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42])
total number of confs: 160
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497531 none CC1=NC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 153, 74, 74, 74, 51, 51, 51, 51, 51, 42, 30, 42, 13, 1, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 201, 201, 153, 153, 74, 51, 51, 51, 51, 51, 30, 30, 1, 51, 51, 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])
total number of confs: 716
number of broken/clashed sets: 60
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497531 none CC1=NC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 25, 25, 25, 40, 40, 40, 40, 40, 43, 43, 83, 124, 201, 201, 201, 201, 201, 40, 1, 1, 2, 2, 2, 7, 7, 25, 40, 40, 40, 40, 40, 83, 83, 201, 40, 40, 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: 543
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497531 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497531
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497531/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497531/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497531
Building REAL300025497532
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497532'
/scratch/stefan/7787277/working/building/REAL300025497532 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497532

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497532/0 /scratch/stefan/7787277/working/building/REAL300025497532 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 393)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/393
`/scratch/stefan/7787277/working/3D/393' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1)

`REAL300025497532.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497532.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497532/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497532 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 34, 57, 152, 152, 152, 152, 152, 1, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 34, 34, 152, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 312
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497532 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 152, 152, 152, 152, 152, 111, 45, 111, 13, 1, 1, 1, 1, 1, 1, 1, 152, 201, 201, 201, 201, 201, 201, 201, 201, 152, 152, 152, 152, 152, 45, 45, 1, 152, 152] 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])
total number of confs: 601
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497532 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 9, 9, 9, 9, 9, 31, 31, 87, 125, 201, 201, 201, 201, 201, 9, 1, 1, 2, 2, 2, 1, 1, 4, 9, 9, 9, 9, 9, 87, 87, 201, 9, 9] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 530
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497532 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497532
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497532/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497532
Building REAL300025497533
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497533'
/scratch/stefan/7787277/working/building/REAL300025497533 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497533

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497533/0 /scratch/stefan/7787277/working/building/REAL300025497533 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 394)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/394
`/scratch/stefan/7787277/working/3D/394' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2[N+](=O)[O-])C1)

`REAL300025497533.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497533.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497533/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497533 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2[N+](=O)[O-])C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 16, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 5, 5, 5, 24, 24, 24, 24, 24, 49, 49, 1, 10, 10, 72, 1, 1, 1, 1, 1, 5, 24, 24, 1, 1] 201
rigid atoms, others: [32, 1, 34, 38, 33, 10, 11, 12, 13, 14, 15, 39, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37])
total number of confs: 246
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497533 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2[N+](=O)[O-])C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 24, 47, 80, 113, 201, 201, 201, 201, 201, 24, 24, 24, 24, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 6, 6, 24, 80, 80, 201, 24, 24, 24, 24, 24, 10, 1, 1, 24, 24] 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])
total number of confs: 529
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497533 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2[N+](=O)[O-])C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'O.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 8, 11, 11, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 35, 13, 1, 1, 1, 1, 1, 1, 1, 50, 72, 72, 72, 72, 72, 99, 99, 99, 201, 201, 201, 201, 201, 201, 201, 72, 35, 35, 1, 72, 72, 72, 72, 72, 99, 201, 201, 72, 72] 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])
total number of confs: 638
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497533 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497533
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497533/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497533
Building REAL300025497534
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497534'
/scratch/stefan/7787277/working/building/REAL300025497534 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497534

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497534/0 /scratch/stefan/7787277/working/building/REAL300025497534 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 395)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/395
`/scratch/stefan/7787277/working/3D/395' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN(C)N=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497534.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497534.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497534/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497534 none CC1=CN(C)N=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 5, 8, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 33, 57, 147, 147, 147, 147, 147, 1, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 33, 33, 147, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 305
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497534 none CC1=CN(C)N=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 5, 8, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 147, 147, 147, 147, 147, 108, 42, 108, 13, 1, 1, 1, 1, 1, 1, 1, 147, 201, 201, 201, 201, 201, 201, 201, 201, 147, 147, 147, 147, 147, 42, 42, 1, 147, 147] 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])
total number of confs: 602
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497534 none CC1=CN(C)N=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 5, 8, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 9, 9, 9, 9, 9, 29, 29, 85, 123, 201, 201, 201, 201, 201, 9, 2, 2, 2, 1, 2, 2, 2, 3, 9, 9, 9, 9, 9, 85, 85, 201, 9, 9] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 542
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497534 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497534
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497534/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497534
Building REAL300025497535
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497535'
/scratch/stefan/7787277/working/building/REAL300025497535 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497535

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497535/0 /scratch/stefan/7787277/working/building/REAL300025497535 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 396)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/396
`/scratch/stefan/7787277/working/3D/396' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC(F)C2)C1)

`REAL300025497535.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497535.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497535/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497535 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC(F)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 7, 7, 6, 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: [5, 1, 5, 14, 24, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 18, 1, 14, 14, 78, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 45, 33, 10, 11, 12, 13, 14, 15, 46, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 183
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497535 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC(F)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 7, 7, 6, 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: [44, 18, 44, 79, 114, 201, 201, 201, 201, 201, 18, 18, 18, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 18, 79, 79, 201, 18, 18, 18, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [35, 36, 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, 45, 46])
total number of confs: 514
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497535 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC(F)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 15, 5, 5, 7, 7, 6, 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: [58, 36, 13, 1, 1, 1, 1, 1, 1, 1, 58, 78, 78, 78, 78, 78, 116, 116, 116, 201, 201, 201, 201, 201, 201, 78, 36, 36, 1, 78, 78, 78, 78, 78, 116, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 78, 78] 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: 658
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497535 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497535
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497535/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497535
Building REAL300025497536
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497536'
/scratch/stefan/7787277/working/building/REAL300025497536 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497536

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497536/0 /scratch/stefan/7787277/working/building/REAL300025497536 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 397)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/397
`/scratch/stefan/7787277/working/3D/397' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025497536.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497536.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497536/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497536 none CN1C=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 21, 84, 84, 84, 84, 84, 1, 23, 23, 23, 23, 23, 23, 19, 19, 5, 1, 1, 1, 1, 1, 12, 12, 84, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 209
number of broken/clashed sets: 46
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497536 none CN1C=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 111, 111, 111, 84, 84, 84, 84, 84, 54, 30, 54, 13, 1, 1, 1, 1, 1, 1, 1, 84, 201, 201, 201, 201, 201, 201, 201, 201, 111, 84, 84, 84, 84, 84, 30, 30, 1, 84, 84] 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])
total number of confs: 787
number of broken/clashed sets: 46
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497536 none CN1C=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 23, 23, 23, 23, 23, 42, 42, 74, 113, 201, 201, 201, 201, 201, 23, 1, 2, 2, 2, 1, 1, 5, 5, 13, 23, 23, 23, 23, 23, 74, 74, 201, 23, 23] 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: 524
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497536 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497536
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497536/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497536
Building REAL300025497537
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497537'
/scratch/stefan/7787277/working/building/REAL300025497537 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497537

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497537/0 /scratch/stefan/7787277/working/building/REAL300025497537 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 398)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/398
`/scratch/stefan/7787277/working/3D/398' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1)

`REAL300025497537.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497537.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497537/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497537 none COCC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 6, 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]
0  hydrogens 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, 24, 18, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 15, 53, 53, 53, 53, 53, 1, 18, 18, 31, 31, 31, 24, 24, 12, 12, 4, 1, 1, 1, 1, 1, 7, 7, 53, 1, 1, 18, 18, 18, 18] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47])
total number of confs: 192
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497537 none COCC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
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, 176, 87, 87, 87, 53, 53, 53, 53, 53, 46, 28, 46, 13, 1, 1, 1, 1, 1, 1, 1, 53, 195, 195, 201, 201, 201, 201, 201, 176, 176, 87, 53, 53, 53, 53, 53, 28, 28, 1, 53, 53, 195, 195, 195, 195] 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: 765
number of broken/clashed sets: 45
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497537 none COCC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 6, 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]
0  hydrogens 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, 7, 1, 1, 1, 7, 15, 15, 15, 18, 18, 18, 18, 18, 19, 19, 54, 95, 195, 195, 195, 195, 195, 18, 1, 1, 14, 14, 14, 7, 7, 7, 7, 15, 18, 18, 18, 18, 18, 54, 54, 195, 18, 18, 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: 469
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497537 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497537
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497537/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497537
Building REAL300025497538
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497538'
/scratch/stefan/7787277/working/building/REAL300025497538 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497538

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497538/0 /scratch/stefan/7787277/working/building/REAL300025497538 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 399)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/399
`/scratch/stefan/7787277/working/3D/399' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1)

`REAL300025497538.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497538.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497538/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497538 none CC1=NC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 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, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 35, 85, 85, 85, 85, 85, 1, 20, 20, 20, 20, 20, 20, 20, 4, 1, 1, 1, 1, 1, 20, 20, 85, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 200
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497538 none CC1=NC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 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, 111, 111, 111, 85, 85, 85, 85, 85, 69, 38, 69, 13, 1, 1, 1, 1, 1, 1, 1, 85, 201, 201, 201, 201, 201, 201, 201, 111, 85, 85, 85, 85, 85, 38, 38, 1, 85, 85] 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])
total number of confs: 514
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497538 none CC1=NC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 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, 9, 9, 9, 20, 20, 20, 20, 20, 52, 52, 103, 140, 201, 201, 201, 201, 201, 20, 1, 2, 2, 2, 2, 2, 2, 9, 20, 20, 20, 20, 20, 103, 103, 201, 20, 20] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 568
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497538 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497538
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497538/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497538
Building REAL300025497539
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497539'
/scratch/stefan/7787277/working/building/REAL300025497539 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497539

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497539/0 /scratch/stefan/7787277/working/building/REAL300025497539 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 400)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/400
`/scratch/stefan/7787277/working/3D/400' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)NCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497539.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497539.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497539/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497539 none NC(=O)NCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
169  conformations in input
total number of sets (complete confs): 169
using faster count positions algorithm for large data
unique positions, atoms: [169, 169, 169, 169, 148, 79, 79, 79, 63, 63, 63, 63, 63, 43, 28, 43, 13, 1, 1, 1, 1, 1, 1, 1, 63, 169, 169, 169, 169, 169, 148, 148, 79, 63, 63, 63, 63, 63, 28, 28, 1, 63, 63] 169
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])
total number of confs: 683
number of broken/clashed sets: 74
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497539 none NC(=O)NCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [29, 29, 29, 28, 19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 14, 63, 63, 63, 63, 63, 1, 29, 29, 29, 28, 28, 19, 19, 5, 1, 1, 1, 1, 1, 7, 7, 63, 1, 1] 169
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 213
number of broken/clashed sets: 74
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497539 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497539
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497539/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497539
Building REAL300025497540
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497540'
/scratch/stefan/7787277/working/building/REAL300025497540 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497540

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497540/0 /scratch/stefan/7787277/working/building/REAL300025497540 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 401)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/401
`/scratch/stefan/7787277/working/3D/401' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1C(=O)CCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497540.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497540.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497540/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497540 none O=C(CN1C(=O)CCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 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]
0  hydrogens 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, 28, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 80, 80, 80, 80, 80, 1, 28, 28, 30, 30, 30, 30, 5, 1, 1, 1, 1, 1, 12, 12, 80, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 229
number of broken/clashed sets: 44
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497540 none O=C(CN1C(=O)CCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 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]
0  hydrogens 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, 201, 201, 201, 201, 201, 201, 201, 80, 80, 80, 80, 80, 51, 30, 51, 13, 1, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 201, 201, 201, 108, 80, 80, 80, 80, 80, 30, 30, 1, 80, 80] 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, 42, 43])
total number of confs: 748
number of broken/clashed sets: 44
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497540 none O=C(CN1C(=O)CCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 4, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 31, 31, 31, 31, 31, 44, 44, 86, 125, 201, 201, 201, 201, 201, 31, 4, 4, 1, 1, 1, 1, 16, 31, 31, 31, 31, 31, 86, 86, 201, 31, 31] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 542
number of broken/clashed sets: 68
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497540 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497540
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497540/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497540
Building REAL300025497541
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497541'
/scratch/stefan/7787277/working/building/REAL300025497541 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497541

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497541/0 /scratch/stefan/7787277/working/building/REAL300025497541 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 402)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/402
`/scratch/stefan/7787277/working/3D/402' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497541.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497541.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497541/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497541 none CC1=CC=CC=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens 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, 26, 37, 37, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 11, 45, 45, 45, 45, 45, 1, 37, 37, 37, 37, 37, 37, 37, 23, 23, 5, 1, 1, 1, 1, 1, 6, 6, 45, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 229
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497541 none CC1=CC=CC=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  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, 201, 201, 153, 63, 63, 63, 45, 45, 45, 45, 45, 37, 26, 37, 12, 1, 1, 1, 1, 1, 1, 1, 45, 201, 201, 201, 201, 201, 201, 201, 153, 153, 63, 45, 45, 45, 45, 45, 26, 26, 1, 45, 45] 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])
total number of confs: 913
number of broken/clashed sets: 50
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497541 none CC1=CC=CC=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total 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, 19, 19, 19, 37, 37, 37, 37, 37, 58, 58, 93, 133, 201, 201, 201, 201, 201, 37, 2, 2, 2, 1, 1, 1, 1, 5, 5, 19, 37, 37, 37, 37, 37, 93, 93, 201, 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: 570
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497541 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497541
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497541/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497541
Building REAL300025497542
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497542'
/scratch/stefan/7787277/working/building/REAL300025497542 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497542

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497542/0 /scratch/stefan/7787277/working/building/REAL300025497542 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 403)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/403
`/scratch/stefan/7787277/working/3D/403' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CC=CS1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497542.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497542.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497542/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497542 none O=C(CCC1=CC=CS1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 14, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 25, 29, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 12, 45, 45, 45, 45, 45, 1, 25, 25, 29, 29, 51, 51, 51, 4, 1, 1, 1, 1, 1, 7, 7, 45, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 224
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497542 none O=C(CCC1=CC=CS1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 14, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [76, 76, 76, 168, 173, 201, 201, 201, 201, 45, 45, 45, 45, 45, 39, 26, 39, 13, 1, 1, 1, 1, 1, 1, 1, 45, 168, 168, 173, 173, 201, 201, 201, 76, 45, 45, 45, 45, 45, 26, 26, 1, 45, 45] 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])
total number of confs: 735
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497542 none O=C(CCC1=CC=CS1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 14, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 23, 23, 51, 51, 51, 51, 51, 72, 72, 84, 135, 201, 201, 201, 201, 201, 51, 7, 7, 3, 3, 1, 1, 1, 23, 51, 51, 51, 51, 51, 84, 84, 201, 51, 51] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 526
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497542 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497542
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497542/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497542
Building REAL300025497543
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497543'
/scratch/stefan/7787277/working/building/REAL300025497543 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497543

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497543/0 /scratch/stefan/7787277/working/building/REAL300025497543 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 404)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/404
`/scratch/stefan/7787277/working/3D/404' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1C=CC=CC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497543.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497543.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497543/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497543 none O=C(CN1C=CC=CC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 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]
0  hydrogens 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, 20, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 22, 87, 87, 87, 87, 87, 1, 20, 20, 24, 24, 24, 24, 5, 1, 1, 1, 1, 1, 14, 14, 87, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 219
number of broken/clashed sets: 44
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497543 none O=C(CN1C=CC=CC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [111, 111, 111, 194, 201, 201, 201, 201, 201, 201, 87, 87, 87, 87, 87, 50, 29, 50, 13, 1, 1, 1, 1, 1, 1, 1, 87, 194, 194, 201, 201, 201, 201, 111, 87, 87, 87, 87, 87, 29, 29, 1, 87, 87] 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, 42, 43])
total number of confs: 730
number of broken/clashed sets: 44
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497543 none O=C(CN1C=CC=CC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 24, 24, 24, 24, 24, 54, 54, 86, 126, 201, 201, 201, 201, 201, 24, 3, 3, 1, 1, 1, 1, 12, 24, 24, 24, 24, 24, 86, 86, 201, 24, 24] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 530
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497543 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497543
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497543/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497543
Building REAL300025497544
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497544'
/scratch/stefan/7787277/working/building/REAL300025497544 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497544

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497544/0 /scratch/stefan/7787277/working/building/REAL300025497544 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 405)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/405
`/scratch/stefan/7787277/working/3D/405' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3CCCC3=C2)C1)

`REAL300025497544.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497544.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497544/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497544 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3CCCC3=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 6, 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, 15, 25, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 1, 15, 15, 70, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 47, 10, 11, 12, 13, 14, 15, 46, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 160
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497544 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3CCCC3=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 6, 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: [36, 15, 36, 75, 115, 201, 201, 201, 201, 201, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 75, 75, 201, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47])
total number of confs: 511
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497544 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3CCCC3=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 6, 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: [55, 38, 11, 1, 1, 1, 1, 1, 1, 1, 55, 70, 70, 70, 70, 70, 83, 83, 83, 201, 201, 201, 201, 201, 201, 201, 201, 70, 38, 38, 1, 70, 70, 70, 70, 70, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 70, 70] 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: 438
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497544 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497544
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497544/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497544
Building REAL300025497545
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497545'
/scratch/stefan/7787277/working/building/REAL300025497545 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497545

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497545/0 /scratch/stefan/7787277/working/building/REAL300025497545 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 406)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/406
`/scratch/stefan/7787277/working/3D/406' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)=NO1)

`REAL300025497545.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497545.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497545/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497545 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', '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, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 6, 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: [43, 20, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 47, 47, 47, 47, 47, 1, 20, 20, 20, 20, 43, 43, 43, 43, 43, 5, 1, 1, 1, 1, 1, 5, 5, 47, 1, 1, 20, 20, 20] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45])
total number of confs: 202
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497545 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', '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, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 6, 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, 193, 193, 88, 88, 88, 47, 47, 47, 47, 47, 42, 29, 42, 13, 1, 1, 1, 1, 1, 1, 1, 47, 193, 193, 193, 193, 201, 201, 201, 201, 201, 88, 47, 47, 47, 47, 47, 29, 29, 1, 47, 47, 193, 193, 193] 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: 495
number of broken/clashed sets: 60
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497545 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', '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, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 8, 12, 7, 7, 7, 7, 7, 6, 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: [5, 1, 1, 1, 1, 11, 11, 11, 20, 20, 20, 20, 20, 27, 27, 55, 86, 193, 193, 193, 193, 193, 20, 1, 1, 1, 1, 5, 6, 6, 5, 5, 11, 20, 20, 20, 20, 20, 55, 55, 193, 20, 20, 2, 2, 2] 201
rigid atoms, others: [1, 2, 3, 4, 23, 24, 25, 26] set([0, 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: 447
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497545 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497545
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497545/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497545
Building REAL300025497546
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497546'
/scratch/stefan/7787277/working/building/REAL300025497546 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497546

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497546/0 /scratch/stefan/7787277/working/building/REAL300025497546 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 407)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/407
`/scratch/stefan/7787277/working/3D/407' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC(C)=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497546.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497546.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497546/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497546 none CC1=NOC(C)=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens 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, 24, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 12, 46, 46, 46, 46, 46, 1, 41, 41, 41, 41, 41, 41, 24, 24, 5, 1, 1, 1, 1, 1, 7, 7, 46, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 44, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 187
number of broken/clashed sets: 58
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497546 none CC1=NOC(C)=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 150, 72, 72, 72, 46, 46, 46, 46, 46, 36, 25, 36, 13, 1, 1, 1, 1, 1, 1, 1, 46, 201, 201, 201, 201, 201, 201, 150, 150, 72, 46, 46, 46, 46, 46, 25, 25, 1, 46, 46] 201
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, 44, 45])
total number of confs: 652
number of broken/clashed sets: 58
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497546 none CC1=NOC(C)=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total 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, 19, 19, 19, 41, 41, 41, 41, 41, 57, 57, 88, 125, 201, 201, 201, 201, 201, 41, 2, 2, 2, 2, 2, 2, 4, 4, 19, 41, 41, 41, 41, 41, 88, 88, 201, 41, 41] 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: 556
number of broken/clashed sets: 58
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497546 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497546
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497546/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497546
Building REAL300025497547
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497547'
/scratch/stefan/7787277/working/building/REAL300025497547 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497547

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497547/0 /scratch/stefan/7787277/working/building/REAL300025497547 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 408)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/408
`/scratch/stefan/7787277/working/3D/408' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC(C)=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497547.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497547.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497547/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497547 none CC1=NNC(C)=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 19, 77, 77, 77, 77, 77, 1, 22, 22, 22, 22, 22, 22, 22, 21, 21, 5, 1, 1, 1, 1, 1, 11, 11, 77, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 197
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497547 none CC1=NNC(C)=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 99, 99, 99, 77, 77, 77, 77, 77, 46, 28, 46, 12, 1, 1, 1, 1, 1, 1, 1, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 99, 77, 77, 77, 77, 77, 28, 28, 1, 77, 77] 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])
total number of confs: 768
number of broken/clashed sets: 35
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497547 none CC1=NNC(C)=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 19, 19, 19, 30, 30, 30, 30, 30, 50, 50, 77, 119, 201, 201, 201, 201, 201, 30, 2, 2, 2, 1, 2, 2, 2, 5, 5, 19, 30, 30, 30, 30, 30, 77, 77, 201, 30, 30] 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: 526
number of broken/clashed sets: 72
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497547 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497547
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497547/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497547
Building REAL300025497548
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497548'
/scratch/stefan/7787277/working/building/REAL300025497548 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497548

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497548/0 /scratch/stefan/7787277/working/building/REAL300025497548 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 409)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/409
`/scratch/stefan/7787277/working/3D/409' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497548.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497548.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497548/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497548 none CC(C)(C)C(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
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, 85, 85, 85, 65, 65, 65, 65, 65, 47, 29, 47, 13, 1, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 195, 195, 85, 65, 65, 65, 65, 65, 29, 29, 1, 65, 65] 201
rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49])
total number of confs: 751
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497548 none CC(C)(C)C(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens 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, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 65, 65, 65, 65, 65, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 21, 21, 5, 1, 1, 1, 1, 1, 8, 8, 65, 1, 1] 201
rigid atoms, others: [48, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 213
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497548 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497548
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497548/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497548
Building REAL300025497549
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497549'
/scratch/stefan/7787277/working/building/REAL300025497549 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497549

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497549/0 /scratch/stefan/7787277/working/building/REAL300025497549 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 410)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/410
`/scratch/stefan/7787277/working/3D/410' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NOC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497549.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497549.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497549/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497549 none CCC1=NOC(C)=C1C(=O)NC1C=CCN(C(=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.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens 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, 22, 22, 22, 22, 22, 22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 46, 46, 46, 46, 46, 1, 41, 41, 41, 41, 41, 22, 22, 22, 5, 1, 1, 1, 1, 1, 5, 5, 46, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 44, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 205
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497549 none CCC1=NOC(C)=C1C(=O)NC1C=CCN(C(=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.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need 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, 181, 181, 181, 181, 86, 86, 86, 46, 46, 46, 46, 46, 40, 29, 40, 13, 1, 1, 1, 1, 1, 1, 1, 46, 201, 201, 201, 201, 201, 181, 181, 181, 86, 46, 46, 46, 46, 46, 29, 29, 1, 46, 46] 201
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, 44, 45])
total number of confs: 540
number of broken/clashed sets: 63
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497549 none CCC1=NOC(C)=C1C(=O)NC1C=CCN(C(=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.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 8, 12, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 22, 22, 22, 22, 22, 27, 27, 50, 76, 181, 181, 181, 181, 181, 22, 5, 5, 5, 5, 5, 2, 2, 2, 8, 22, 22, 22, 22, 22, 50, 50, 181, 22, 22] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 413
number of broken/clashed sets: 63
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497549 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497549
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497549/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497549
Building REAL300025497550
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497550'
/scratch/stefan/7787277/working/building/REAL300025497550 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497550

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497550/0 /scratch/stefan/7787277/working/building/REAL300025497550 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 411)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/411
`/scratch/stefan/7787277/working/3D/411' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497550.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497550.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497550/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497550 none O=C(CCC1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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: [4, 4, 4, 19, 24, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 38, 38, 38, 38, 38, 1, 19, 19, 26, 26, 44, 44, 44, 44, 44, 44, 44, 44, 44, 4, 1, 1, 1, 1, 1, 5, 5, 38, 1, 1] 201
rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48])
total number of confs: 230
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497550 none O=C(CCC1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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: [61, 61, 61, 162, 150, 201, 201, 201, 201, 201, 38, 38, 38, 38, 38, 36, 25, 36, 12, 1, 1, 1, 1, 1, 1, 1, 38, 162, 162, 169, 169, 201, 201, 201, 201, 201, 201, 201, 201, 201, 61, 38, 38, 38, 38, 38, 25, 25, 1, 38, 38] 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, 50])
total number of confs: 859
number of broken/clashed sets: 53
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497550 none O=C(CCC1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 5, 5, 12, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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: [32, 7, 5, 1, 1, 1, 1, 1, 1, 1, 32, 32, 44, 44, 44, 44, 44, 47, 47, 89, 133, 201, 201, 201, 201, 201, 44, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 44, 44, 44, 44, 44, 89, 89, 201, 44, 44] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 39, 35, 36, 38, 37, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 556
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497550 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497550
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497550/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497550
Building REAL300025497551
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497551'
/scratch/stefan/7787277/working/building/REAL300025497551 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497551

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497551/0 /scratch/stefan/7787277/working/building/REAL300025497551 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 412)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/412
`/scratch/stefan/7787277/working/3D/412' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497551.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497551.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497551/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497551 none CC1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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: [23, 23, 23, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 33, 74, 74, 74, 74, 74, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 1, 19, 19, 74, 1, 1, 23, 23] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46])
total number of confs: 214
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497551 none CC1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 96, 96, 96, 74, 74, 74, 74, 74, 60, 36, 60, 13, 1, 1, 1, 1, 1, 1, 1, 74, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 96, 74, 74, 74, 74, 74, 36, 36, 1, 74, 74, 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])
total number of confs: 616
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497551 none CC1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 1, 8, 8, 8, 23, 23, 23, 23, 23, 51, 51, 98, 136, 201, 201, 201, 201, 201, 23, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 23, 23, 23, 23, 23, 98, 98, 201, 23, 23, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 46, 24, 33, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 560
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497551 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497551
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497551/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497551
Building REAL300025497552
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497552'
/scratch/stefan/7787277/working/building/REAL300025497552 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497552

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497552/0 /scratch/stefan/7787277/working/building/REAL300025497552 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 413)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/413
`/scratch/stefan/7787277/working/3D/413' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=NOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497552.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497552.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497552/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497552 none CC(C)C1=NOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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: [19, 7, 19, 7, 7, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 45, 128, 128, 128, 128, 128, 1, 7, 19, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 25, 25, 128, 1, 1, 7] 201
rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45])
total number of confs: 306
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497552 none CC(C)C1=NOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 176, 201, 176, 176, 176, 175, 175, 175, 128, 128, 128, 128, 128, 94, 42, 94, 13, 1, 1, 1, 1, 1, 1, 1, 128, 176, 201, 201, 201, 201, 201, 201, 201, 175, 128, 128, 128, 128, 128, 42, 42, 1, 128, 128, 176] 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: 701
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497552 none CC(C)C1=NOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 5, 1, 8, 12, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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: [5, 1, 5, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 22, 22, 57, 89, 176, 176, 176, 176, 176, 7, 1, 5, 5, 5, 5, 5, 5, 5, 3, 7, 7, 7, 7, 7, 57, 57, 176, 7, 7, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 45, 26] set([0, 2, 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: 426
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497552 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497552
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497552/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497552
Building REAL300025497553
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497553'
/scratch/stefan/7787277/working/building/REAL300025497553 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497553

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497553/0 /scratch/stefan/7787277/working/building/REAL300025497553 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 414)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/414
`/scratch/stefan/7787277/working/3D/414' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025497553.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497553.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497553/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497553 none CCN1C=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 6, 6, 6, 6, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 35, 94, 94, 94, 94, 94, 1, 6, 15, 15, 15, 15, 15, 6, 6, 5, 1, 1, 1, 1, 1, 19, 19, 94, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 241
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497553 none CCN1C=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 115, 115, 115, 115, 115, 115, 115, 94, 94, 94, 94, 94, 78, 40, 78, 13, 1, 1, 1, 1, 1, 1, 1, 94, 115, 201, 201, 201, 201, 201, 115, 115, 115, 94, 94, 94, 94, 94, 40, 40, 1, 94, 94] 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])
total number of confs: 884
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497553 none CCN1C=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 2, 2, 2, 6, 6, 6, 6, 6, 16, 16, 39, 62, 115, 115, 115, 115, 115, 6, 1, 5, 5, 5, 5, 5, 1, 1, 2, 6, 6, 6, 6, 6, 39, 39, 115, 6, 6] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 297
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497553 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497553
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497553/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497553
Building REAL300025497554
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497554'
/scratch/stefan/7787277/working/building/REAL300025497554 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497554

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497554/0 /scratch/stefan/7787277/working/building/REAL300025497554 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 415)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/415
`/scratch/stefan/7787277/working/3D/415' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497554.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497554.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497554/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497554 none CC(C)CCCCCC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens need rotated
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, 167, 201, 167, 184, 75, 75, 75, 50, 50, 50, 50, 50, 45, 30, 45, 13, 1, 1, 1, 1, 1, 1, 1, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 184, 184, 75, 50, 50, 50, 50, 50, 30, 30, 1, 50, 50] 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: 1511
number of broken/clashed sets: 62
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497554 none CC(C)CCCCCC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens 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, 28, 28, 33, 28, 23, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 50, 50, 50, 50, 50, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 23, 23, 4, 1, 1, 1, 1, 1, 5, 5, 50, 1, 1] 201
rigid atoms, others: [16, 15, 10, 11, 12, 13, 46, 45, 48, 49, 14, 54, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52])
total number of confs: 304
number of broken/clashed sets: 62
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497554 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497554
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497554/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497554
Building REAL300025497555
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497555'
/scratch/stefan/7787277/working/building/REAL300025497555 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497555

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497555/0 /scratch/stefan/7787277/working/building/REAL300025497555 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 416)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/416
`/scratch/stefan/7787277/working/3D/416' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(Cl)=CS2)C1)

`REAL300025497555.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497555.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497555/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497555 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(Cl)=CS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 16, 1, 14, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 38, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 1, 18, 18, 119, 1, 1, 1, 1, 1, 4, 16, 16, 1, 1] 201
rigid atoms, others: [32, 1, 36, 37, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35])
total number of confs: 230
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497555 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(Cl)=CS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 16, 1, 14, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 16, 36, 74, 113, 201, 201, 201, 201, 201, 16, 16, 16, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 16, 74, 74, 201, 16, 16, 16, 16, 16, 7, 1, 1, 16, 16] 201
rigid atoms, others: [34, 35, 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, 36, 37])
total number of confs: 488
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497555 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(Cl)=CS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'Cl', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 16, 1, 14, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 43, 13, 1, 1, 1, 1, 1, 1, 1, 89, 119, 119, 119, 119, 119, 181, 181, 181, 201, 201, 201, 201, 201, 119, 43, 43, 1, 119, 119, 119, 119, 119, 181, 201, 201, 119, 119] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 604
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497555 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497555
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497555/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497555
Building REAL300025497556
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497556'
/scratch/stefan/7787277/working/building/REAL300025497556 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497556

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497556/0 /scratch/stefan/7787277/working/building/REAL300025497556 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 417)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/417
`/scratch/stefan/7787277/working/3D/417' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC(Cl)=C2)C1)

`REAL300025497556.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497556.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497556/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497556 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC(Cl)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 14, 1, 16, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 14, 22, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 1, 14, 14, 95, 1, 1, 1, 1, 1, 5, 13, 13, 1, 1] 201
rigid atoms, others: [32, 1, 36, 37, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35])
total number of confs: 176
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497556 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC(Cl)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 14, 1, 16, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 13, 33, 70, 102, 201, 201, 201, 201, 201, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 13, 70, 70, 201, 13, 13, 13, 13, 13, 5, 1, 1, 13, 13] 201
rigid atoms, others: [34, 35, 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, 36, 37])
total number of confs: 494
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497556 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC(Cl)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'Cl', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 14, 1, 16, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 47, 13, 1, 1, 1, 1, 1, 1, 1, 70, 95, 95, 95, 95, 95, 116, 116, 116, 201, 201, 201, 201, 201, 95, 47, 47, 1, 95, 95, 95, 95, 95, 116, 201, 201, 95, 95] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 520
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497556 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497556
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497556/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497556
Building REAL300025497557
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497557'
/scratch/stefan/7787277/working/building/REAL300025497557 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497557

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497557/0 /scratch/stefan/7787277/working/building/REAL300025497557 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 418)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/418
`/scratch/stefan/7787277/working/3D/418' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(Cl)SC=C2)C1)

`REAL300025497557.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497557.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497557/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497557 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(Cl)SC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 16, 14, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 33, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 16, 16, 103, 1, 1, 1, 1, 1, 5, 15, 15, 1, 1] 201
rigid atoms, others: [32, 1, 36, 37, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35])
total number of confs: 199
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497557 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(Cl)SC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 16, 14, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 15, 34, 65, 104, 201, 201, 201, 201, 201, 15, 15, 15, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 15, 65, 65, 201, 15, 15, 15, 15, 15, 6, 1, 1, 15, 15] 201
rigid atoms, others: [34, 35, 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, 36, 37])
total number of confs: 468
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497557 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(Cl)SC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'S.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 16, 14, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 43, 13, 1, 1, 1, 1, 1, 1, 1, 77, 103, 103, 103, 103, 103, 133, 133, 133, 201, 201, 201, 201, 201, 103, 43, 43, 1, 103, 103, 103, 103, 103, 133, 201, 201, 103, 103] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 516
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497557 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497557
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497557/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497557
Building REAL300025497558
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497558'
/scratch/stefan/7787277/working/building/REAL300025497558 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497558

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497558/0 /scratch/stefan/7787277/working/building/REAL300025497558 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 419)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/419
`/scratch/stefan/7787277/working/3D/419' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCCC(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497558.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497558.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497558/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497558 none CCCCCC(C)CC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 179, 165, 179, 55, 55, 55, 53, 53, 53, 53, 53, 46, 28, 46, 13, 1, 1, 1, 1, 1, 1, 1, 53, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 179, 179, 179, 165, 165, 55, 53, 53, 53, 53, 53, 28, 28, 1, 53, 53] 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: 815
number of broken/clashed sets: 77
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497558 none CCCCCC(C)CC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens 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, 17, 11, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 12, 53, 53, 53, 53, 53, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 17, 17, 17, 17, 11, 11, 3, 1, 1, 1, 1, 1, 6, 6, 53, 1, 1] 201
rigid atoms, others: [16, 15, 10, 11, 12, 13, 46, 45, 48, 49, 14, 54, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52])
total number of confs: 180
number of broken/clashed sets: 77
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497558 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497558
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497558/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497558
Building REAL300025497559
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497559'
/scratch/stefan/7787277/working/building/REAL300025497559 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497559

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497559/0 /scratch/stefan/7787277/working/building/REAL300025497559 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 420)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/420
`/scratch/stefan/7787277/working/3D/420' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CN=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025497559.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497559.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497559/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497559 none COC1=CN=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 30, 52, 156, 156, 156, 156, 156, 1, 9, 9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 30, 30, 156, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 305
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497559 none COC1=CN=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 200, 200, 200, 156, 156, 156, 156, 156, 108, 44, 108, 13, 1, 1, 1, 1, 1, 1, 1, 156, 201, 201, 201, 201, 201, 201, 200, 156, 156, 156, 156, 156, 44, 44, 1, 156, 156] 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])
total number of confs: 599
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497559 none COC1=CN=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 30, 30, 81, 114, 201, 201, 201, 201, 201, 9, 1, 2, 2, 2, 1, 1, 3, 9, 9, 9, 9, 9, 81, 81, 201, 9, 9] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 26, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 518
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497559 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497559
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497559/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497559
Building REAL300025497560
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497560'
/scratch/stefan/7787277/working/building/REAL300025497560 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497560

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497560/0 /scratch/stefan/7787277/working/building/REAL300025497560 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 421)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/421
`/scratch/stefan/7787277/working/3D/421' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CS1)

`REAL300025497560.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497560.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497560/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497560 none CC1=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 45, 26, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 11, 52, 52, 52, 52, 52, 1, 45, 45, 45, 45, 45, 45, 26, 26, 5, 1, 1, 1, 1, 1, 6, 6, 52, 1, 1, 45, 45] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43])
total number of confs: 196
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497560 none CC1=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 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
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, 77, 77, 77, 52, 52, 52, 52, 52, 41, 28, 41, 13, 1, 1, 1, 1, 1, 1, 1, 52, 201, 201, 201, 201, 201, 201, 166, 166, 77, 52, 52, 52, 52, 52, 28, 28, 1, 52, 52, 201, 201] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 703
number of broken/clashed sets: 59
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497560 none CC1=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 14, 7, 7, 7, 7, 7, 6, 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
201  conformations 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, 24, 24, 24, 45, 45, 45, 45, 45, 54, 54, 94, 129, 201, 201, 201, 201, 201, 45, 1, 1, 1, 2, 2, 2, 6, 6, 24, 45, 45, 45, 45, 45, 94, 94, 201, 45, 45, 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: 578
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497560 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497560
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497560/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497560
Building REAL300025497561
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497561'
/scratch/stefan/7787277/working/building/REAL300025497561 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497561

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497561/0 /scratch/stefan/7787277/working/building/REAL300025497561 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 422)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/422
`/scratch/stefan/7787277/working/3D/422' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C)

`REAL300025497561.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497561.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497561/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497561 none CCOC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [193, 193, 193, 148, 148, 148, 98, 98, 98, 98, 98, 67, 38, 67, 13, 1, 1, 1, 1, 1, 1, 1, 98, 193, 201, 201, 193, 193, 193, 193, 193, 193, 148, 98, 98, 98, 98, 98, 38, 38, 1, 98, 98, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 777
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: REAL300025497561 none CCOC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 98, 98, 98, 98, 98, 1, 12, 21, 21, 13, 13, 13, 13, 13, 12, 5, 1, 1, 1, 1, 1, 10, 10, 98, 1, 1, 21, 21, 21, 21, 21, 21, 21] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 223
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497561 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497561
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497561/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497561
Building REAL300025497562
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497562'
/scratch/stefan/7787277/working/building/REAL300025497562 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497562

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497562/0 /scratch/stefan/7787277/working/building/REAL300025497562 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 423)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/423
`/scratch/stefan/7787277/working/3D/423' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCOCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497562.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497562.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497562/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497562 none C#CCOCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 149, 139, 138, 59, 59, 59, 51, 51, 51, 51, 51, 40, 25, 40, 12, 1, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 139, 139, 138, 138, 59, 51, 51, 51, 51, 51, 25, 25, 1, 51, 51] 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])
total number of confs: 863
number of broken/clashed sets: 132
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497562 none C#CCOCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 17, 12, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 15, 51, 51, 51, 51, 51, 1, 42, 42, 42, 12, 12, 11, 11, 3, 1, 1, 1, 1, 1, 8, 8, 51, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 247
number of broken/clashed sets: 132
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497562 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497562
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497562/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497562
Building REAL300025497563
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497563'
/scratch/stefan/7787277/working/building/REAL300025497563 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497563

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497563/0 /scratch/stefan/7787277/working/building/REAL300025497563 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 424)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/424
`/scratch/stefan/7787277/working/3D/424' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCOC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497563.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497563.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497563/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497563 none C#CCOC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 168, 157, 113, 157, 113, 113, 72, 72, 72, 72, 72, 54, 29, 53, 13, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 157, 157, 157, 157, 113, 72, 72, 72, 72, 72, 29, 29, 1, 72, 72] 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])
total number of confs: 799
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497563 none C#CCOC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 15, 9, 4, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 24, 72, 72, 72, 72, 72, 1, 35, 35, 35, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 13, 13, 72, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 264
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497563 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497563
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497563/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497563
Building REAL300025497564
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497564'
/scratch/stefan/7787277/working/building/REAL300025497564 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497564

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497564/0 /scratch/stefan/7787277/working/building/REAL300025497564 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 425)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/425
`/scratch/stefan/7787277/working/3D/425' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[N@@H+]1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497564.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497564.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497564/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497564 none CC(C)[N@@H+]1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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]
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, 7, 7, 7, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 11, 18, 18, 18, 18, 18, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 7, 7, 18, 1, 1] 28
rigid atoms, others: [45, 11, 47, 44, 43, 12, 13, 14, 15, 16, 17, 51, 52, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 57
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497564 none CC(C)[N@@H+]1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 26, 26, 26, 18, 18, 18, 18, 18, 17, 16, 17, 11, 1, 1, 1, 1, 1, 1, 1, 18, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 26, 18, 18, 18, 18, 18, 16, 16, 1, 18, 18] 28
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: 86
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497564 none CC(C)[N@@H+]1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
28  conformations in input
total number of sets (complete confs): 28
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 10, 10, 18, 23, 28, 28, 28, 28, 28, 7, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 18, 18, 28, 7, 7] 28
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 39, 40, 35, 41, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 96
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497564 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497564/1 /scratch/stefan/7787277/working/building/REAL300025497564 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 426)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/426
`/scratch/stefan/7787277/working/3D/426' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[N@H+]1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497564.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497564.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497564/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497564 none CC(C)[N@H+]1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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]
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, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1] 4
rigid atoms, others: [45, 11, 47, 44, 43, 12, 13, 14, 15, 16, 17, 51, 52, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 23
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497564 none CC(C)[N@H+]1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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]
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, 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, 4, 4, 4, 4, 1, 4, 4] 4
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: 10
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497564 none CC(C)[N@H+]1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 9, 6, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
4  conformations in input
total number of sets (complete confs): 4
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 4
rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 39, 40, 35, 41, 36, 38, 37] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 17
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497564 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497564
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497564/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497564/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497564
Building REAL300025497565
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497565'
/scratch/stefan/7787277/working/building/REAL300025497565 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497565

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497565/0 /scratch/stefan/7787277/working/building/REAL300025497565 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 427)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/427
`/scratch/stefan/7787277/working/3D/427' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCOCC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497565.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497565.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497565/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497565 none O=C(CCOCC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need 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, 8, 8, 12, 28, 42, 42, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 34, 34, 34, 34, 34, 1, 8, 8, 8, 8, 28, 28, 42, 42, 42, 42, 42, 3, 1, 1, 1, 1, 1, 4, 4, 34, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 206
number of broken/clashed sets: 162
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497565 none O=C(CCOCC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 106, 106, 117, 157, 201, 201, 34, 34, 34, 34, 34, 34, 26, 34, 13, 1, 1, 1, 1, 1, 1, 1, 34, 106, 106, 106, 106, 157, 157, 201, 201, 201, 201, 201, 36, 34, 34, 34, 34, 34, 26, 26, 1, 34, 34] 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])
total number of confs: 806
number of broken/clashed sets: 162
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497565 none O=C(CCOCC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 22, 14, 6, 1, 1, 1, 1, 40, 40, 42, 42, 42, 42, 42, 42, 42, 66, 101, 201, 201, 201, 201, 201, 42, 29, 29, 22, 22, 6, 6, 1, 1, 1, 1, 1, 40, 42, 42, 42, 42, 42, 66, 66, 201, 42, 42] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8] 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 514
number of broken/clashed sets: 162
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497565 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497565
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497565/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497565
Building REAL300025497566
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497566'
/scratch/stefan/7787277/working/building/REAL300025497566 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497566

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497566/0 /scratch/stefan/7787277/working/building/REAL300025497566 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 428)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/428
`/scratch/stefan/7787277/working/3D/428' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COC1CCOC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497566.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497566.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497566/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497566 none O=C(COC1CCOC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 12, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 11, 22, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 12, 60, 60, 60, 60, 60, 1, 11, 11, 36, 36, 36, 36, 36, 36, 36, 5, 1, 1, 1, 1, 1, 6, 6, 60, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 189
number of broken/clashed sets: 81
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497566 none O=C(COC1CCOC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 12, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [82, 82, 82, 145, 158, 201, 201, 201, 201, 60, 60, 60, 60, 60, 49, 30, 49, 13, 1, 1, 1, 1, 1, 1, 1, 60, 145, 145, 201, 201, 201, 201, 201, 201, 201, 82, 60, 60, 60, 60, 60, 30, 30, 1, 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])
total number of confs: 775
number of broken/clashed sets: 81
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497566 none O=C(COC1CCOC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 12, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 12, 5, 1, 1, 1, 1, 1, 1, 26, 26, 36, 36, 36, 36, 36, 43, 43, 80, 123, 201, 201, 201, 201, 201, 36, 12, 12, 1, 1, 1, 1, 1, 1, 1, 26, 36, 36, 36, 36, 36, 80, 80, 201, 36, 36] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 524
number of broken/clashed sets: 81
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497566 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497566
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497566/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497566
Building REAL300025497567
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497567'
/scratch/stefan/7787277/working/building/REAL300025497567 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497567

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497567/0 /scratch/stefan/7787277/working/building/REAL300025497567 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 429)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/429
`/scratch/stefan/7787277/working/3D/429' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)NC(N)=O)

`REAL300025497567.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497567.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497567/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497567 none CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)NC(N)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 4, 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: [200, 199, 151, 151, 151, 114, 114, 114, 114, 114, 70, 31, 70, 13, 1, 1, 1, 1, 1, 1, 1, 114, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 151, 114, 114, 114, 114, 114, 31, 31, 1, 114, 114, 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])
total number of confs: 692
number of broken/clashed sets: 80
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497567 none CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)NC(N)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 18, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 31, 114, 114, 114, 114, 114, 1, 26, 33, 33, 33, 26, 26, 26, 26, 18, 18, 5, 1, 1, 1, 1, 1, 16, 16, 114, 1, 1, 33, 33, 33] 201
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 41, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45])
total number of confs: 333
number of broken/clashed sets: 80
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497567 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497567
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497567/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497567
Building REAL300025497568
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497568'
/scratch/stefan/7787277/working/building/REAL300025497568 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497568

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497568/0 /scratch/stefan/7787277/working/building/REAL300025497568 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 430)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/430
`/scratch/stefan/7787277/working/3D/430' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C(F)F)CC2)C1)

`REAL300025497568.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497568.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497568/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497568 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C(F)F)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 15, 15, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 22, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 4, 4, 4, 15, 39, 39, 15, 15, 1, 13, 12, 78, 1, 1, 1, 1, 1, 4, 39, 15, 15, 15, 15, 1, 1] 201
rigid atoms, others: [32, 1, 39, 40, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38])
total number of confs: 271
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497568 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C(F)F)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 15, 15, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 15, 34, 58, 89, 186, 186, 186, 186, 186, 15, 15, 15, 15, 6, 6, 1, 6, 1, 1, 7, 7, 1, 1, 15, 58, 58, 186, 15, 15, 15, 15, 15, 6, 7, 1, 1, 1, 1, 15, 15] 201
rigid atoms, others: [35, 36, 37, 38, 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, 39, 40])
total number of confs: 456
number of broken/clashed sets: 49
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497568 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C(F)F)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 15, 15, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 36, 12, 1, 1, 1, 1, 1, 1, 1, 61, 78, 78, 78, 78, 78, 114, 114, 114, 186, 201, 201, 186, 186, 78, 36, 36, 1, 78, 78, 78, 78, 78, 114, 201, 186, 186, 186, 186, 78, 78] 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: 677
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497568 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497568
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497568/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497568
Building REAL300025497569
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497569'
/scratch/stefan/7787277/working/building/REAL300025497569 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497569

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497569/0 /scratch/stefan/7787277/working/building/REAL300025497569 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 431)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/431
`/scratch/stefan/7787277/working/3D/431' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC3(CC3)C2)C1)

`REAL300025497569.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497569.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497569/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497569 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC3(CC3)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [5, 1, 5, 12, 20, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 1, 12, 12, 63, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 49, 50, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 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])
total number of confs: 159
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497569 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC3(CC3)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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, 18, 45, 80, 112, 201, 201, 201, 201, 201, 18, 18, 18, 18, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 18, 80, 80, 201, 18, 18, 18, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [16, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 49, 50])
total number of confs: 513
number of broken/clashed sets: 29
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497569 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC3(CC3)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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, 13, 1, 1, 1, 1, 1, 1, 1, 42, 63, 63, 63, 63, 63, 92, 92, 92, 201, 201, 201, 201, 201, 201, 201, 63, 29, 29, 1, 63, 63, 63, 63, 63, 92, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 63, 63] 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: 636
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497569 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497569
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497569/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497569
Building REAL300025497570
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497570'
/scratch/stefan/7787277/working/building/REAL300025497570 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497570

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497570/0 /scratch/stefan/7787277/working/building/REAL300025497570 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 432)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/432
`/scratch/stefan/7787277/working/3D/432' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497570.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497570.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497570/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497570 none C=CCC(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 172, 90, 172, 172, 90, 90, 47, 47, 47, 47, 47, 39, 26, 39, 13, 1, 1, 1, 1, 1, 1, 1, 47, 201, 201, 201, 201, 201, 172, 172, 172, 172, 172, 172, 90, 47, 47, 47, 47, 47, 26, 26, 1, 47, 47] 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])
total number of confs: 872
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: REAL300025497570 none C=CCC(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [40, 27, 12, 4, 12, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 47, 47, 47, 47, 47, 1, 40, 40, 40, 27, 27, 12, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 10, 10, 47, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 248
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497570 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497570
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497570/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497570
Building REAL300025497571
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497571'
/scratch/stefan/7787277/working/building/REAL300025497571 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497571

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497571/0 /scratch/stefan/7787277/working/building/REAL300025497571 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 433)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/433
`/scratch/stefan/7787277/working/3D/433' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C(F)C2=CC=CC=C2)C1)

`REAL300025497571.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497571.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497571/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497571 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C(F)C2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 15, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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, 19, 32, 87, 87, 87, 87, 87, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 17, 17, 17, 17, 17, 1, 19, 19, 87, 1, 1, 1, 1, 1, 5, 13, 17, 17, 17, 17, 17, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 10, 11, 12, 13, 14, 15, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 226
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497571 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C(F)C2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 15, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [45, 17, 45, 92, 129, 201, 201, 201, 201, 201, 17, 17, 17, 17, 6, 6, 3, 6, 1, 3, 1, 1, 1, 1, 1, 1, 17, 92, 92, 201, 17, 17, 17, 17, 17, 6, 3, 1, 1, 1, 1, 1, 17, 17] 201
rigid atoms, others: [37, 38, 39, 40, 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, 42, 43])
total number of confs: 559
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497571 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C(F)C2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 15, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [68, 40, 13, 1, 1, 1, 1, 1, 1, 1, 68, 87, 87, 87, 87, 87, 142, 142, 142, 201, 201, 201, 201, 201, 201, 201, 87, 40, 40, 1, 87, 87, 87, 87, 87, 142, 201, 201, 201, 201, 201, 201, 87, 87] 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: 762
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497571 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497571
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497571/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497571
Building REAL300025497572
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497572'
/scratch/stefan/7787277/working/building/REAL300025497572 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497572

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497572/0 /scratch/stefan/7787277/working/building/REAL300025497572 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 434)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/434
`/scratch/stefan/7787277/working/3D/434' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC23CCC3)C1)

`REAL300025497572.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497572.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497572/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497572 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC23CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 20, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 23, 23, 23, 23, 1, 13, 13, 72, 1, 1, 1, 1, 1, 5, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1] 201
rigid atoms, others: [32, 1, 43, 44, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 179
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497572 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC23CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 23, 53, 88, 115, 201, 201, 201, 201, 201, 23, 23, 23, 23, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 23, 88, 88, 201, 23, 23, 23, 23, 23, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 201
rigid atoms, others: [34, 35, 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, 43, 44])
total number of confs: 524
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497572 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC23CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 36, 13, 1, 1, 1, 1, 1, 1, 1, 52, 72, 72, 72, 72, 72, 100, 100, 100, 201, 201, 201, 201, 201, 72, 36, 36, 1, 72, 72, 72, 72, 72, 100, 201, 201, 201, 201, 201, 201, 201, 201, 201, 72, 72] 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: 636
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497572 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497572
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497572/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497572
Building REAL300025497573
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497573'
/scratch/stefan/7787277/working/building/REAL300025497573 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497573

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497573/0 /scratch/stefan/7787277/working/building/REAL300025497573 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 435)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/435
`/scratch/stefan/7787277/working/3D/435' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2CC(=O)NC(=O)N2)C1)

`REAL300025497573.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497573.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497573/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497573 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2CC(=O)NC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 1, 7, 17, 31, 99, 99, 99, 99, 99, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 1, 17, 17, 99, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 41, 10, 11, 12, 13, 14, 15, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40])
total number of confs: 213
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497573 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2CC(=O)NC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 17, 35, 69, 105, 201, 201, 201, 201, 201, 17, 17, 17, 17, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 69, 69, 201, 17, 17, 17, 17, 17, 8, 1, 1, 1, 1, 17, 17] 201
rigid atoms, others: [37, 38, 39, 40, 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, 41, 42])
total number of confs: 475
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497573 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2CC(=O)NC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 1, 11, 8, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7, 7]
dock 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [73, 39, 12, 1, 1, 1, 1, 1, 1, 1, 73, 99, 99, 99, 99, 99, 139, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 99, 39, 39, 1, 99, 99, 99, 99, 99, 139, 201, 201, 201, 201, 99, 99] 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: 621
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497573 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497573
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497573/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497573
Building REAL300025497574
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497574'
/scratch/stefan/7787277/working/building/REAL300025497574 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497574

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497574/0 /scratch/stefan/7787277/working/building/REAL300025497574 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 436)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/436
`/scratch/stefan/7787277/working/3D/436' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1C=C(Cl)C=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497574.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497574.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497574/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497574 none O=C(CN1C=C(Cl)C=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 1, 16, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 20, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 23, 81, 81, 81, 81, 81, 1, 20, 20, 29, 29, 5, 1, 1, 1, 1, 1, 13, 13, 81, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 222
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497574 none O=C(CN1C=C(Cl)C=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 1, 16, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [110, 110, 110, 201, 201, 201, 201, 201, 201, 81, 81, 81, 81, 81, 51, 28, 51, 12, 1, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 201, 110, 81, 81, 81, 81, 81, 28, 28, 1, 81, 81] 201
rigid atoms, others: [38, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 804
number of broken/clashed sets: 47
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497574 none O=C(CN1C=C(Cl)C=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 1, 16, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 17, 17, 29, 29, 29, 29, 29, 47, 47, 81, 120, 201, 201, 201, 201, 201, 29, 7, 7, 1, 1, 17, 29, 29, 29, 29, 29, 81, 81, 201, 29, 29] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 536
number of broken/clashed sets: 47
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497574 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497574
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497574/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497574
Building REAL300025497575
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497575'
/scratch/stefan/7787277/working/building/REAL300025497575 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497575

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497575/0 /scratch/stefan/7787277/working/building/REAL300025497575 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 437)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/437
`/scratch/stefan/7787277/working/3D/437' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CN=C1)

`REAL300025497575.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497575.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497575/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497575 none CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7]
0  hydrogens 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, 124, 69, 69, 69, 52, 52, 52, 52, 52, 42, 27, 42, 13, 1, 1, 1, 1, 1, 1, 1, 52, 132, 201, 201, 201, 201, 132, 132, 132, 132, 124, 124, 69, 52, 52, 52, 52, 52, 27, 27, 1, 52, 52, 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])
total number of confs: 680
number of broken/clashed sets: 74
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497575 none CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7]
0  hydrogens 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, 24, 24, 24, 34, 34, 34, 34, 34, 51, 51, 89, 127, 201, 201, 201, 201, 201, 34, 1, 1, 1, 1, 1, 3, 3, 3, 2, 8, 8, 24, 34, 34, 34, 34, 34, 89, 89, 201, 34, 34, 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: 564
number of broken/clashed sets: 74
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497575 none CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1C=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 52, 52, 52, 52, 52, 1, 21, 34, 34, 34, 34, 21, 21, 21, 21, 12, 12, 4, 1, 1, 1, 1, 1, 6, 6, 52, 1, 1, 34, 34, 34] 201
rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 43, 21, 38, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46])
total number of confs: 197
number of broken/clashed sets: 74
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497575 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497575
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497575/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497575
Building REAL300025497576
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497576'
/scratch/stefan/7787277/working/building/REAL300025497576 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497576

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497576/0 /scratch/stefan/7787277/working/building/REAL300025497576 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 438)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/438
`/scratch/stefan/7787277/working/3D/438' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)=N1)

`REAL300025497576.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497576.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497576/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497576 none CCN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 34, 106, 106, 106, 106, 106, 1, 8, 8, 8, 18, 18, 18, 18, 18, 8, 5, 1, 1, 1, 1, 1, 18, 18, 106, 1, 1, 8, 8, 8] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46])
total number of confs: 258
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497576 none CCN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 139, 139, 139, 106, 106, 106, 106, 106, 85, 43, 85, 13, 1, 1, 1, 1, 1, 1, 1, 106, 141, 141, 141, 201, 201, 201, 201, 201, 141, 139, 106, 106, 106, 106, 106, 43, 43, 1, 106, 106, 141, 141, 141] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46])
total number of confs: 809
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497576 none CCN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 25, 25, 48, 71, 141, 141, 141, 141, 141, 8, 1, 1, 1, 5, 5, 5, 5, 5, 1, 3, 8, 8, 8, 8, 8, 48, 48, 141, 8, 8, 2, 2, 2] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 24, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 346
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497576 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497576
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497576/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497576
Building REAL300025497577
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497577'
/scratch/stefan/7787277/working/building/REAL300025497577 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497577

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497577/0 /scratch/stefan/7787277/working/building/REAL300025497577 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 439)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/439
`/scratch/stefan/7787277/working/3D/439' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=NN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497577.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497577.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497577/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497577 none CC1=CC=NN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 22, 22, 19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 27, 101, 101, 101, 101, 101, 1, 22, 22, 22, 22, 22, 19, 19, 5, 1, 1, 1, 1, 1, 15, 15, 101, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 237
number of broken/clashed sets: 46
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497577 none CC1=CC=NN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 101, 101, 101, 101, 101, 60, 30, 60, 13, 1, 1, 1, 1, 1, 1, 1, 101, 201, 201, 201, 201, 201, 201, 201, 132, 101, 101, 101, 101, 101, 30, 30, 1, 101, 101] 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])
total number of confs: 743
number of broken/clashed sets: 46
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497577 none CC1=CC=NN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 8, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 12, 12, 12, 22, 22, 22, 22, 22, 44, 44, 74, 115, 201, 201, 201, 201, 201, 22, 2, 2, 2, 1, 1, 4, 4, 12, 22, 22, 22, 22, 22, 74, 74, 201, 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: 507
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497577 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497577
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497577/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497577
Building REAL300025497578
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497578'
/scratch/stefan/7787277/working/building/REAL300025497578 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497578

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497578/0 /scratch/stefan/7787277/working/building/REAL300025497578 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 440)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/440
`/scratch/stefan/7787277/working/3D/440' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1)

`REAL300025497578.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497578.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497578/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497578 none CCCN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [29, 27, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 26, 78, 78, 78, 78, 78, 1, 12, 12, 29, 29, 29, 29, 29, 27, 27, 12, 5, 1, 1, 1, 1, 1, 15, 15, 78, 1, 1, 12] 201
rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46])
total number of confs: 253
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497578 none CCCN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 139, 139, 139, 84, 84, 84, 78, 78, 78, 78, 78, 68, 38, 68, 13, 1, 1, 1, 1, 1, 1, 1, 78, 139, 139, 201, 201, 201, 201, 201, 201, 201, 139, 84, 78, 78, 78, 78, 78, 38, 38, 1, 78, 78, 139] 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: 746
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497578 none CCCN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 5, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 29, 29, 47, 68, 139, 139, 139, 139, 139, 12, 1, 1, 7, 7, 7, 7, 7, 5, 5, 1, 5, 12, 12, 12, 12, 12, 47, 47, 139, 12, 12, 1] 201
rigid atoms, others: [34, 3, 4, 5, 6, 2, 46, 25, 26] set([0, 1, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 339
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497578 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497578
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497578/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497578
Building REAL300025497579
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497579'
/scratch/stefan/7787277/working/building/REAL300025497579 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497579

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497579/0 /scratch/stefan/7787277/working/building/REAL300025497579 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 441)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/441
`/scratch/stefan/7787277/working/3D/441' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(C3CC3)=NO2)C1)

`REAL300025497579.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497579.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497579/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025497579 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(C3CC3)=NO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 19, 34, 110, 110, 110, 110, 110, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 6, 21, 21, 6, 6, 1, 19, 19, 110, 1, 1, 1, 1, 1, 5, 6, 21, 21, 21, 21, 21, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 10, 11, 12, 13, 14, 15, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 251
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.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: REAL300025497579 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(C3CC3)=NO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [44, 21, 44, 87, 123, 201, 201, 201, 201, 201, 21, 21, 21, 21, 12, 12, 11, 12, 11, 11, 1, 1, 1, 1, 11, 11, 21, 87, 87, 201, 21, 21, 21, 21, 21, 12, 11, 1, 1, 1, 1, 1, 21, 21] 201
rigid atoms, others: [37, 38, 39, 40, 41, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43])
total number of confs: 516
number of broken/clashed sets: 13
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497579 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(C3CC3)=NO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 6, 14, 35, 54, 134, 134, 134, 134, 134, 6, 6, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 11, 11, 1, 1, 6, 35, 35, 134, 6, 6, 6, 6, 6, 2, 1, 11, 11, 11, 11, 11, 6, 6] 201
rigid atoms, others: [36, 16, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 308
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497579 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(C3CC3)=NO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 5, 5, 5, 8, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [87, 42, 13, 1, 1, 1, 1, 1, 1, 1, 87, 110, 110, 110, 110, 110, 134, 134, 134, 135, 135, 135, 201, 201, 135, 135, 110, 42, 42, 1, 110, 110, 110, 110, 110, 134, 135, 201, 201, 201, 201, 201, 110, 110] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 689
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497579 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497579
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497579/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497579
Building REAL300025497580
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497580'
/scratch/stefan/7787277/working/building/REAL300025497580 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497580

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497580/0 /scratch/stefan/7787277/working/building/REAL300025497580 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 442)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/442
`/scratch/stefan/7787277/working/3D/442' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NO1)

`REAL300025497580.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497580.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497580/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497580 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 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: [38, 22, 22, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 17, 79, 79, 79, 79, 79, 1, 22, 22, 22, 38, 38, 38, 38, 38, 4, 1, 1, 1, 1, 1, 9, 9, 79, 1, 1, 22] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42])
total number of confs: 233
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497580 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 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, 183, 183, 117, 117, 117, 79, 79, 79, 79, 79, 57, 27, 57, 13, 1, 1, 1, 1, 1, 1, 1, 79, 183, 183, 183, 201, 201, 201, 201, 201, 117, 79, 79, 79, 79, 79, 27, 27, 1, 79, 79, 183] 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: 581
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497580 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 12, 7, 7, 7, 7, 7, 6, 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: [6, 1, 1, 1, 1, 10, 10, 10, 22, 22, 22, 22, 22, 30, 30, 56, 92, 183, 183, 183, 183, 183, 22, 1, 1, 1, 6, 6, 6, 6, 6, 10, 22, 22, 22, 22, 22, 56, 56, 183, 22, 22, 1] 201
rigid atoms, others: [1, 2, 3, 4, 42, 23, 24, 25] set([0, 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: 435
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497580 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497580
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497580/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497580
Building REAL300025497581
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497581'
/scratch/stefan/7787277/working/building/REAL300025497581 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497581

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497581/0 /scratch/stefan/7787277/working/building/REAL300025497581 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 443)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/443
`/scratch/stefan/7787277/working/3D/443' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CSC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497581.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497581.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497581/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497581 none O=C(CC1=CSC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 23, 94, 94, 94, 94, 94, 1, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 14, 14, 94, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 39, 8, 9, 10, 11, 12, 13, 14, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 220
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497581 none O=C(CC1=CSC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [122, 122, 122, 201, 201, 201, 201, 201, 94, 94, 94, 94, 94, 56, 30, 56, 13, 1, 1, 1, 1, 1, 1, 1, 94, 201, 201, 201, 201, 122, 94, 94, 94, 94, 94, 30, 30, 1, 94, 94] 201
rigid atoms, others: [37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 795
number of broken/clashed sets: 39
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497581 none O=C(CC1=CSC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 14, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 21, 21, 21, 21, 21, 52, 52, 87, 124, 201, 201, 201, 201, 201, 21, 3, 3, 1, 1, 9, 21, 21, 21, 21, 21, 87, 87, 201, 21, 21] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 527
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497581 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497581
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497581/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497581
Building REAL300025497582
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497582'
/scratch/stefan/7787277/working/building/REAL300025497582 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497582

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497582/0 /scratch/stefan/7787277/working/building/REAL300025497582 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 444)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/444
`/scratch/stefan/7787277/working/3D/444' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COC(C3CC3)=N2)C1)

`REAL300025497582.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497582.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497582/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025497582 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COC(C3CC3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 12, 1, 5, 5, 5, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 31, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 24, 24, 5, 1, 17, 17, 104, 1, 1, 1, 1, 1, 5, 5, 24, 24, 24, 24, 24, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 10, 11, 12, 13, 14, 15, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 243
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.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: REAL300025497582 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COC(C3CC3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 12, 1, 5, 5, 5, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [48, 24, 48, 85, 124, 201, 201, 201, 201, 201, 24, 24, 24, 24, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 24, 85, 85, 201, 24, 24, 24, 24, 24, 12, 12, 1, 1, 1, 1, 1, 24, 24] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 515
number of broken/clashed sets: 7
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497582 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COC(C3CC3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 12, 1, 5, 5, 5, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 12, 25, 42, 121, 121, 121, 121, 121, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 12, 12, 1, 5, 25, 25, 121, 5, 5, 5, 5, 5, 2, 1, 12, 12, 12, 12, 12, 5, 5] 201
rigid atoms, others: [36, 16, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 261
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497582 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COC(C3CC3)=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 12, 1, 5, 5, 5, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 41, 13, 1, 1, 1, 1, 1, 1, 1, 81, 104, 104, 104, 104, 104, 121, 121, 121, 121, 121, 121, 121, 201, 201, 121, 104, 41, 41, 1, 104, 104, 104, 104, 104, 121, 121, 201, 201, 201, 201, 201, 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: 697
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497582 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497582
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497582/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497582
Building REAL300025497583
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497583'
/scratch/stefan/7787277/working/building/REAL300025497583 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497583

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497583/0 /scratch/stefan/7787277/working/building/REAL300025497583 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 445)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/445
`/scratch/stefan/7787277/working/3D/445' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2C[C@@H]2C2=CC=CC=C2)C1)

`REAL300025497583.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497583.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497583/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025497583 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2C[C@@H]2C2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 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: [7, 1, 7, 18, 28, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 4, 4, 4, 29, 29, 29, 29, 29, 39, 39, 29, 39, 39, 1, 18, 18, 72, 1, 1, 1, 1, 1, 4, 29, 29, 39, 39, 36, 39, 39, 1, 1] 201
rigid atoms, others: [1, 34, 35, 36, 37, 33, 10, 11, 12, 13, 14, 15, 46, 47, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 269
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: REAL300025497583 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2C[C@@H]2C2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 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: [69, 39, 69, 121, 151, 201, 201, 201, 201, 201, 39, 39, 39, 39, 20, 20, 4, 20, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 39, 121, 121, 201, 39, 39, 39, 39, 39, 20, 4, 4, 1, 1, 1, 1, 1, 39, 39] 201
rigid atoms, others: [41, 42, 43, 44, 45, 21, 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, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47])
total number of confs: 604
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497583 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2C[C@@H]2C2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 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: [59, 29, 59, 108, 138, 201, 201, 201, 201, 201, 29, 29, 29, 29, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 4, 4, 1, 4, 4, 29, 108, 108, 201, 29, 29, 29, 29, 29, 11, 1, 1, 4, 4, 2, 4, 4, 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])
total number of confs: 590
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497583 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2C[C@@H]2C2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 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: [67, 36, 12, 1, 1, 1, 1, 1, 1, 1, 67, 72, 72, 72, 72, 72, 96, 96, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 72, 36, 36, 1, 72, 72, 72, 72, 72, 96, 201, 201, 201, 201, 201, 201, 201, 72, 72] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497583 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497583
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497583/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497583
Building REAL300025497584
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497584'
/scratch/stefan/7787277/working/building/REAL300025497584 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497584

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497584/0 /scratch/stefan/7787277/working/building/REAL300025497584 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 446)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/446
`/scratch/stefan/7787277/working/3D/446' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1)

`REAL300025497584.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497584.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497584/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497584 none COCC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [25, 18, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 26, 90, 90, 90, 90, 90, 1, 5, 5, 25, 25, 25, 18, 18, 5, 5, 1, 1, 1, 1, 1, 14, 14, 90, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 234
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497584 none COCC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 98, 98, 98, 98, 98, 98, 90, 90, 90, 90, 90, 68, 37, 68, 13, 1, 1, 1, 1, 1, 1, 1, 90, 98, 98, 201, 201, 201, 201, 201, 98, 98, 90, 90, 90, 90, 90, 37, 37, 1, 90, 90] 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])
total number of confs: 791
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497584 none COCC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 8, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 11, 11, 20, 33, 98, 98, 98, 98, 98, 5, 1, 1, 14, 14, 14, 8, 8, 1, 1, 5, 5, 5, 5, 5, 20, 20, 98, 5, 5] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 25, 26] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 219
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497584 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497584
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497584/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497584
Building REAL300025497585
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497585'
/scratch/stefan/7787277/working/building/REAL300025497585 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497585

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497585/0 /scratch/stefan/7787277/working/building/REAL300025497585 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 447)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/447
`/scratch/stefan/7787277/working/3D/447' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3C=CC=NN32)C1)

`REAL300025497585.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497585.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497585/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497585 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3C=CC=NN32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 7, 7, 6, 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, 28, 49, 160, 160, 160, 160, 160, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 1, 28, 28, 160, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 305
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497585 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3C=CC=NN32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 7, 7, 6, 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: [33, 10, 33, 84, 119, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 84, 84, 201, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 524
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497585 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3C=CC=NN32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 8, 8, 5, 7, 7, 6, 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: [112, 45, 13, 1, 1, 1, 1, 1, 1, 1, 112, 160, 160, 160, 160, 160, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 160, 45, 45, 1, 160, 160, 160, 160, 160, 201, 201, 201, 201, 201, 201, 160, 160] 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: 592
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497585 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497585
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497585/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497585
Building REAL300025497586
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497586'
/scratch/stefan/7787277/working/building/REAL300025497586 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497586

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497586/0 /scratch/stefan/7787277/working/building/REAL300025497586 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 448)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/448
`/scratch/stefan/7787277/working/3D/448' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497586.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497586.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497586/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497586 none CN(C)C(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  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, 88, 88, 88, 71, 71, 71, 71, 71, 49, 29, 49, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 201, 158, 158, 88, 71, 71, 71, 71, 71, 29, 29, 1, 71, 71] 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])
total number of confs: 751
number of broken/clashed sets: 116
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497586 none CN(C)C(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 33, 13, 30, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 14, 71, 71, 71, 71, 71, 1, 33, 33, 33, 33, 33, 33, 13, 13, 4, 1, 1, 1, 1, 1, 7, 7, 71, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 217
number of broken/clashed sets: 116
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497586 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497586
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497586/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497586
Building REAL300025497587
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497587'
/scratch/stefan/7787277/working/building/REAL300025497587 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497587

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497587/0 /scratch/stefan/7787277/working/building/REAL300025497587 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 449)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/449
`/scratch/stefan/7787277/working/3D/449' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1)

`REAL300025497587.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497587.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497587/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497587 none C=CCN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 6, 6, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 26, 80, 80, 80, 80, 80, 1, 6, 6, 25, 25, 25, 16, 16, 6, 5, 1, 1, 1, 1, 1, 15, 15, 80, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 235
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497587 none C=CCN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 105, 105, 105, 80, 80, 80, 80, 80, 58, 39, 58, 13, 1, 1, 1, 1, 1, 1, 1, 80, 107, 107, 201, 201, 201, 201, 201, 107, 105, 80, 80, 80, 80, 80, 39, 39, 1, 80, 80] 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])
total number of confs: 840
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497587 none C=CCN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 6, 1, 1, 1, 1, 1, 2, 2, 3, 6, 6, 6, 6, 6, 13, 13, 29, 44, 107, 107, 107, 107, 107, 6, 1, 1, 11, 11, 11, 6, 6, 1, 3, 6, 6, 6, 6, 6, 29, 29, 107, 6, 6] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 25, 26] set([0, 1, 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])
total number of confs: 270
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497587 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497587
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497587/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497587
Building REAL300025497588
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497588'
/scratch/stefan/7787277/working/building/REAL300025497588 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497588

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497588/0 /scratch/stefan/7787277/working/building/REAL300025497588 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 450)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/450
`/scratch/stefan/7787277/working/3D/450' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025497588.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497588.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497588/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497588 none CN1C=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 33, 57, 154, 154, 154, 154, 154, 1, 10, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 1, 33, 33, 154, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 40, 23, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 315
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497588 none CN1C=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 154, 154, 154, 154, 154, 114, 43, 114, 13, 1, 1, 1, 1, 1, 1, 1, 154, 201, 201, 201, 201, 201, 201, 201, 154, 154, 154, 154, 154, 43, 43, 1, 154, 154] 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])
total number of confs: 599
number of broken/clashed sets: 29
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497588 none CN1C=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 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, 3, 3, 3, 10, 10, 10, 10, 10, 30, 30, 83, 122, 201, 201, 201, 201, 201, 10, 1, 2, 2, 2, 1, 1, 3, 10, 10, 10, 10, 10, 83, 83, 201, 10, 10] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 525
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497588 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497588
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497588/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497588
Building REAL300025497589
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497589'
/scratch/stefan/7787277/working/building/REAL300025497589 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497589

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497589/0 /scratch/stefan/7787277/working/building/REAL300025497589 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 451)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/451
`/scratch/stefan/7787277/working/3D/451' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=CN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497589.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497589.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497589/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497589 none CC1=NC=CN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 40, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 18, 70, 70, 70, 70, 70, 1, 40, 40, 40, 40, 40, 23, 23, 5, 1, 1, 1, 1, 1, 11, 11, 70, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 222
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497589 none CC1=NC=CN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 94, 94, 94, 70, 70, 70, 70, 70, 45, 28, 45, 13, 1, 1, 1, 1, 1, 1, 1, 70, 201, 201, 201, 201, 201, 176, 176, 94, 70, 70, 70, 70, 70, 28, 28, 1, 70, 70] 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])
total number of confs: 698
number of broken/clashed sets: 52
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497589 none CC1=NC=CN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 24, 24, 24, 40, 40, 40, 40, 40, 56, 56, 86, 126, 201, 201, 201, 201, 201, 40, 2, 2, 2, 1, 1, 6, 6, 24, 40, 40, 40, 40, 40, 86, 86, 201, 40, 40] 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: 553
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497589 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497589/1 /scratch/stefan/7787277/working/building/REAL300025497589 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 452)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/452
`/scratch/stefan/7787277/working/3D/452' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=[NH+]C=CN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497589.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497589.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497589/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497589 none CC1=[NH+]C=CN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [15, 15, 15, 15, 15, 15, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 11, 11, 11, 11, 11, 1, 15, 15, 15, 15, 15, 13, 13, 4, 1, 1, 1, 1, 1, 6, 6, 11, 1, 1] 24
rigid atoms, others: [35, 36, 37, 38, 39, 44, 10, 11, 12, 13, 14, 15, 16, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 75
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497589 none CC1=[NH+]C=CN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 24, 24, 24, 24, 22, 15, 15, 15, 11, 11, 11, 11, 11, 10, 8, 10, 7, 1, 1, 1, 1, 1, 1, 1, 11, 24, 24, 24, 24, 24, 22, 22, 15, 11, 11, 11, 11, 11, 8, 8, 1, 11, 11] 24
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, 43, 44])
total number of confs: 83
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497589 none CC1=[NH+]C=CN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 6, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 10, 15, 15, 15, 15, 15, 15, 15, 23, 23, 24, 24, 24, 24, 24, 15, 2, 2, 2, 1, 1, 3, 3, 10, 15, 15, 15, 15, 15, 23, 23, 24, 15, 15] 24
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: 95
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497589 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497589
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497589/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497589/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497589
Building REAL300025497590
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497590'
/scratch/stefan/7787277/working/building/REAL300025497590 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497590

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497590/0 /scratch/stefan/7787277/working/building/REAL300025497590 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 453)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/453
`/scratch/stefan/7787277/working/3D/453' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1)

`REAL300025497590.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497590.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497590/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497590 none CC1=CC=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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: [30, 30, 30, 30, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 20, 40, 40, 40, 40, 40, 1, 30, 30, 30, 30, 30, 30, 30, 16, 16, 5, 1, 1, 1, 1, 1, 14, 14, 40, 1, 1, 30] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45])
total number of confs: 173
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497590 none CC1=CC=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 128, 54, 54, 54, 40, 40, 40, 40, 40, 38, 29, 38, 13, 1, 1, 1, 1, 1, 1, 1, 40, 201, 201, 201, 201, 201, 201, 201, 128, 128, 54, 40, 40, 40, 40, 40, 29, 29, 1, 40, 40, 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])
total number of confs: 669
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497590 none CC1=CC=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 11, 11, 11, 30, 30, 30, 30, 30, 59, 59, 101, 132, 201, 201, 201, 201, 201, 30, 1, 1, 2, 2, 2, 1, 1, 4, 4, 11, 30, 30, 30, 30, 30, 101, 101, 201, 30, 30, 1] 201
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: 578
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497590 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497590
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497590/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497590
Building REAL300025497591
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497591'
/scratch/stefan/7787277/working/building/REAL300025497591 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497591

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497591/0 /scratch/stefan/7787277/working/building/REAL300025497591 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 454)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/454
`/scratch/stefan/7787277/working/3D/454' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1)

`REAL300025497591.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497591.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497591/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497591 none NC(=O)C1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 17, 18, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 33, 78, 78, 78, 78, 78, 1, 17, 17, 18, 18, 17, 5, 1, 1, 1, 1, 1, 19, 19, 78, 1, 1, 17, 17] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42])
total number of confs: 192
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497591 none NC(=O)C1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 200, 201, 200, 200, 98, 98, 98, 78, 78, 78, 78, 78, 63, 38, 63, 13, 1, 1, 1, 1, 1, 1, 1, 78, 200, 200, 201, 201, 200, 98, 78, 78, 78, 78, 78, 38, 38, 1, 78, 78, 200, 200] 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: 487
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497591 none NC(=O)C1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CN1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 6, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6]
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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 47, 47, 93, 132, 200, 200, 200, 200, 200, 17, 1, 1, 3, 3, 1, 5, 17, 17, 17, 17, 17, 93, 93, 200, 17, 17, 1, 1] 201
rigid atoms, others: [1, 3, 4, 5, 6, 41, 42, 25, 26, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 557
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497591 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497591
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497591/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497591
Building REAL300025497592
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497592'
/scratch/stefan/7787277/working/building/REAL300025497592 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497592

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497592/0 /scratch/stefan/7787277/working/building/REAL300025497592 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 455)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/455
`/scratch/stefan/7787277/working/3D/455' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497592.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497592.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497592/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497592 none CCN1C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 25, 88, 88, 88, 88, 88, 1, 22, 22, 22, 22, 22, 12, 12, 12, 5, 1, 1, 1, 1, 1, 14, 14, 88, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 228
number of broken/clashed sets: 41
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497592 none CCN1C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 149, 149, 129, 129, 129, 88, 88, 88, 88, 88, 58, 28, 58, 13, 1, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 201, 201, 149, 149, 149, 129, 88, 88, 88, 88, 88, 28, 28, 1, 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])
total number of confs: 725
number of broken/clashed sets: 41
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497592 none CCN1C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 12, 12, 12, 12, 12, 29, 29, 55, 82, 149, 149, 149, 149, 149, 12, 3, 3, 3, 3, 3, 1, 1, 1, 4, 12, 12, 12, 12, 12, 55, 55, 149, 12, 12] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 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, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 369
number of broken/clashed sets: 41
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497592 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497592
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497592/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497592
Building REAL300025497593
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497593'
/scratch/stefan/7787277/working/building/REAL300025497593 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497593

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497593/0 /scratch/stefan/7787277/working/building/REAL300025497593 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 456)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/456
`/scratch/stefan/7787277/working/3D/456' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)N1C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497593.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497593.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497593/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497593 none CC(C)N1C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens 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, 16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 32, 122, 122, 122, 122, 122, 1, 29, 29, 29, 29, 29, 29, 29, 16, 16, 16, 5, 1, 1, 1, 1, 1, 17, 17, 122, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 289
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497593 none CC(C)N1C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
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, 161, 161, 161, 122, 122, 122, 122, 122, 75, 31, 75, 13, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 161, 122, 122, 122, 122, 122, 31, 31, 1, 122, 122] 201
rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47])
total number of confs: 531
number of broken/clashed sets: 48
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497593 none CC(C)N1C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens 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, 6, 6, 6, 16, 16, 16, 16, 16, 39, 39, 74, 118, 201, 201, 201, 201, 201, 16, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 6, 16, 16, 16, 16, 16, 74, 74, 201, 16, 16] 201
rigid atoms, others: [1, 34, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 509
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497593 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497593
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497593/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497593
Building REAL300025497594
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497594'
/scratch/stefan/7787277/working/building/REAL300025497594 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497594

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497594/0 /scratch/stefan/7787277/working/building/REAL300025497594 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 457)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/457
`/scratch/stefan/7787277/working/3D/457' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NC=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497594.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497594.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497594/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497594 none CCC1=NC=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 26, 26, 26, 5, 26, 26, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 52, 52, 52, 52, 52, 1, 45, 45, 45, 45, 45, 5, 26, 5, 1, 1, 1, 1, 1, 7, 8, 52, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 44, 10, 11, 12, 13, 14, 15, 16, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 246
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497594 none CCC1=NC=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 86, 201, 201, 86, 86, 86, 52, 52, 52, 52, 52, 41, 27, 41, 13, 1, 1, 1, 1, 1, 1, 1, 52, 201, 201, 201, 201, 201, 86, 201, 86, 52, 52, 52, 52, 52, 27, 27, 1, 52, 52] 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, 43, 44])
total number of confs: 645
number of broken/clashed sets: 67
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497594 none CCC1=NC=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 8, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 26, 26, 26, 36, 36, 68, 103, 201, 201, 201, 201, 201, 26, 5, 5, 5, 5, 5, 1, 1, 9, 26, 26, 26, 26, 26, 68, 68, 201, 26, 26] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 33] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 500
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497594 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497594
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497594/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497594
Building REAL300025497595
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497595'
/scratch/stefan/7787277/working/building/REAL300025497595 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497595

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497595/0 /scratch/stefan/7787277/working/building/REAL300025497595 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 458)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/458
`/scratch/stefan/7787277/working/3D/458' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCCOC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497595.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497595.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497595/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497595 none O=C(CC1CCCOC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 23, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 15, 69, 69, 69, 69, 69, 1, 23, 23, 35, 35, 35, 35, 35, 35, 35, 35, 35, 5, 1, 1, 1, 1, 1, 8, 8, 69, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 226
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497595 none O=C(CC1CCCOC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [110, 110, 110, 190, 201, 201, 201, 201, 201, 69, 69, 69, 69, 69, 51, 28, 51, 13, 1, 1, 1, 1, 1, 1, 1, 69, 190, 190, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 69, 69, 69, 69, 69, 28, 28, 1, 69, 69] 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])
total number of confs: 764
number of broken/clashed sets: 50
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497595 none O=C(CC1CCCOC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 12, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 1, 23, 23, 35, 35, 35, 35, 35, 47, 47, 83, 125, 201, 201, 201, 201, 201, 35, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 35, 35, 35, 35, 35, 83, 83, 201, 35, 35] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 527
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497595 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497595
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497595/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497595
Building REAL300025497596
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497596'
/scratch/stefan/7787277/working/building/REAL300025497596 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497596

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497596/0 /scratch/stefan/7787277/working/building/REAL300025497596 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 459)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/459
`/scratch/stefan/7787277/working/3D/459' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC=CCC2)C1)

`REAL300025497596.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497596.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497596/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497596 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC=CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 14, 26, 81, 81, 81, 81, 81, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 17, 1, 14, 14, 81, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1] 201
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 14, 15, 46, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 188
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497596 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC=CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 17, 35, 72, 104, 201, 201, 201, 201, 201, 17, 17, 17, 17, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 17, 72, 72, 201, 17, 17, 17, 17, 17, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 201
rigid atoms, others: [35, 36, 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, 46, 47])
total number of confs: 493
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497596 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC=CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 39, 13, 1, 1, 1, 1, 1, 1, 1, 61, 81, 81, 81, 81, 81, 115, 115, 115, 201, 201, 201, 201, 201, 201, 81, 39, 39, 1, 81, 81, 81, 81, 81, 115, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 81, 81] 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: 645
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497596 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497596
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497596/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497596
Building REAL300025497597
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497597'
/scratch/stefan/7787277/working/building/REAL300025497597 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497597

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497597/0 /scratch/stefan/7787277/working/building/REAL300025497597 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 460)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/460
`/scratch/stefan/7787277/working/3D/460' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025497597.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497597.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497597/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497597 none CC1=NC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 55, 145, 145, 145, 145, 145, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 32, 32, 145, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 301
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497597 none CC1=NC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 145, 145, 145, 145, 145, 104, 43, 104, 13, 1, 1, 1, 1, 1, 1, 1, 145, 201, 201, 201, 201, 201, 201, 201, 145, 145, 145, 145, 145, 43, 43, 1, 145, 145] 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])
total number of confs: 601
number of broken/clashed sets: 29
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497597 none CC1=NC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 31, 31, 84, 121, 201, 201, 201, 201, 201, 9, 1, 2, 2, 2, 1, 1, 4, 9, 9, 9, 9, 9, 84, 84, 201, 9, 9] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 29, 30] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 527
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497597 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497597
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497597/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497597
Building REAL300025497598
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497598'
/scratch/stefan/7787277/working/building/REAL300025497598 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497598

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497598/0 /scratch/stefan/7787277/working/building/REAL300025497598 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 461)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/461
`/scratch/stefan/7787277/working/3D/461' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497598.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497598.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497598/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497598 none CCC(C)C(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 176, 201, 176, 176, 175, 71, 71, 71, 50, 50, 50, 50, 50, 38, 26, 38, 13, 1, 1, 1, 1, 1, 1, 1, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 176, 175, 175, 71, 50, 50, 50, 50, 50, 26, 26, 1, 50, 50] 201
rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49])
total number of confs: 819
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: REAL300025497598 none CCC(C)C(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens 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, 36, 22, 36, 22, 22, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 50, 50, 50, 50, 50, 1, 37, 37, 37, 37, 37, 36, 36, 36, 36, 22, 19, 19, 4, 1, 1, 1, 1, 1, 5, 5, 50, 1, 1] 201
rigid atoms, others: [48, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 216
number of broken/clashed sets: 83
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497598 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497598
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497598/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497598
Building REAL300025497599
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497599'
/scratch/stefan/7787277/working/building/REAL300025497599 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497599

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497599/0 /scratch/stefan/7787277/working/building/REAL300025497599 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 462)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/462
`/scratch/stefan/7787277/working/3D/462' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCN1CCCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497599.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497599.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497599/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497599 none O=C(CCN1CCCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 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: [4, 4, 4, 21, 24, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 34, 94, 94, 94, 94, 94, 1, 21, 21, 24, 24, 36, 36, 36, 36, 36, 36, 4, 1, 1, 1, 1, 1, 21, 21, 94, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 287
number of broken/clashed sets: 57
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497599 none O=C(CCN1CCCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 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: [116, 116, 116, 194, 195, 201, 201, 201, 201, 201, 94, 94, 94, 94, 94, 70, 30, 69, 13, 1, 1, 1, 1, 1, 1, 1, 94, 194, 194, 195, 195, 201, 201, 201, 201, 201, 201, 116, 94, 94, 94, 94, 94, 30, 30, 1, 94, 94] 201
rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47])
total number of confs: 742
number of broken/clashed sets: 57
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497599 none O=C(CCN1CCCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 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: [23, 9, 6, 1, 1, 1, 1, 1, 1, 1, 23, 23, 36, 36, 36, 36, 36, 46, 46, 88, 123, 201, 201, 201, 201, 201, 36, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 23, 36, 36, 36, 36, 36, 88, 88, 201, 36, 36] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 540
number of broken/clashed sets: 57
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497599 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497599
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497599/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497599
Building REAL300025497600
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497600'
/scratch/stefan/7787277/working/building/REAL300025497600 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497600

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497600/0 /scratch/stefan/7787277/working/building/REAL300025497600 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 463)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/463
`/scratch/stefan/7787277/working/3D/463' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNS(=O)(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497600.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497600.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497600/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497600 none CNS(=O)(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 14, 11, 11, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 182, 201, 201, 108, 108, 108, 86, 86, 86, 86, 86, 58, 27, 58, 13, 1, 1, 1, 1, 1, 1, 1, 86, 201, 201, 201, 201, 182, 182, 108, 86, 86, 86, 86, 86, 27, 27, 1, 86, 86] 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])
total number of confs: 807
number of broken/clashed sets: 100
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497600 none CNS(=O)(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 14, 11, 11, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 4, 7, 6, 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]
0  hydrogens 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, 12, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 18, 86, 86, 86, 86, 86, 1, 31, 31, 31, 31, 12, 12, 5, 1, 1, 1, 1, 1, 9, 9, 86, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 238
number of broken/clashed sets: 100
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497600 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497600
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497600/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497600
Building REAL300025497601
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497601'
/scratch/stefan/7787277/working/building/REAL300025497601 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497601

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497601/0 /scratch/stefan/7787277/working/building/REAL300025497601 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 464)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/464
`/scratch/stefan/7787277/working/3D/464' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3NC=CC=C23)C1)

`REAL300025497601.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497601.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497601/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497601 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3NC=CC=C23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 7, 7, 6, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 19, 34, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 1, 5, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 1, 19, 19, 102, 1, 1, 1, 1, 1, 5, 26, 26, 26, 26, 26, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 225
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497601 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3NC=CC=C23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 7, 7, 6, 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, 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: [62, 26, 62, 106, 140, 201, 201, 201, 201, 201, 26, 26, 26, 26, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 106, 106, 201, 26, 26, 26, 26, 26, 10, 1, 1, 1, 1, 1, 26, 26] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 574
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497601 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3NC=CC=C23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 7, 7, 6, 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, 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: [81, 42, 13, 1, 1, 1, 1, 1, 1, 1, 81, 102, 102, 102, 102, 102, 139, 139, 139, 201, 201, 201, 201, 201, 201, 201, 201, 102, 42, 42, 1, 102, 102, 102, 102, 102, 139, 201, 201, 201, 201, 201, 102, 102] 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: 543
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497601 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497601
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497601/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497601
Building REAL300025497602
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497602'
/scratch/stefan/7787277/working/building/REAL300025497602 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497602

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497602/0 /scratch/stefan/7787277/working/building/REAL300025497602 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 465)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/465
`/scratch/stefan/7787277/working/3D/465' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCN1C=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497602.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497602.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497602/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497602 none O=C(CCCN1C=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 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]
0  hydrogens 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, 15, 17, 22, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 19, 69, 69, 69, 69, 69, 1, 15, 15, 20, 20, 21, 20, 31, 31, 31, 5, 1, 1, 1, 1, 1, 11, 11, 69, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 233
number of broken/clashed sets: 77
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497602 none O=C(CCCN1C=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [92, 92, 92, 188, 157, 193, 201, 201, 201, 201, 69, 69, 69, 69, 69, 47, 27, 47, 13, 1, 1, 1, 1, 1, 1, 1, 69, 188, 188, 193, 193, 183, 169, 201, 201, 201, 92, 69, 69, 69, 69, 69, 27, 27, 1, 69, 69] 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])
total number of confs: 905
number of broken/clashed sets: 77
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497602 none O=C(CCCN1C=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 1, 8, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 15, 10, 6, 1, 1, 1, 1, 1, 1, 25, 25, 31, 31, 31, 31, 31, 41, 41, 76, 115, 201, 201, 201, 201, 201, 31, 15, 15, 10, 10, 6, 6, 1, 1, 1, 25, 31, 31, 31, 31, 31, 76, 76, 201, 31, 31] 201
rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 545
number of broken/clashed sets: 77
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497602 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497602
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497602/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497602
Building REAL300025497603
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497603'
/scratch/stefan/7787277/working/building/REAL300025497603 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497603

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497603/0 /scratch/stefan/7787277/working/building/REAL300025497603 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 466)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/466
`/scratch/stefan/7787277/working/3D/466' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=NC=CS1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497603.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497603.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497603/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497603 none O=C(CCC1=NC=CS1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 14, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 19, 24, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 10, 42, 42, 42, 42, 42, 1, 19, 19, 24, 24, 45, 45, 4, 1, 1, 1, 1, 1, 6, 6, 42, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 190
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497603 none O=C(CCC1=NC=CS1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 14, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 130, 144, 201, 201, 201, 201, 42, 42, 42, 42, 42, 34, 25, 34, 12, 1, 1, 1, 1, 1, 1, 1, 42, 130, 130, 144, 144, 201, 201, 63, 42, 42, 42, 42, 42, 25, 25, 1, 42, 42] 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])
total number of confs: 670
number of broken/clashed sets: 47
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497603 none O=C(CCC1=NC=CS1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'S.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 14, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 3, 1, 1, 1, 1, 1, 1, 32, 32, 45, 45, 45, 45, 45, 51, 51, 97, 139, 201, 201, 201, 201, 201, 45, 9, 9, 3, 3, 1, 1, 32, 45, 45, 45, 45, 45, 97, 97, 201, 45, 45] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 597
number of broken/clashed sets: 47
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497603 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497603
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497603/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497603
Building REAL300025497604
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497604'
/scratch/stefan/7787277/working/building/REAL300025497604 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497604

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497604/0 /scratch/stefan/7787277/working/building/REAL300025497604 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 467)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/467
`/scratch/stefan/7787277/working/3D/467' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497604.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497604.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497604/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497604 none COCCC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
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, 196, 134, 196, 134, 134, 94, 94, 94, 94, 94, 65, 31, 65, 13, 1, 1, 1, 1, 1, 1, 1, 94, 201, 201, 201, 201, 201, 199, 199, 196, 196, 196, 196, 134, 94, 94, 94, 94, 94, 31, 31, 1, 94, 94] 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])
total number of confs: 783
number of broken/clashed sets: 89
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497604 none COCCC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 21, 16, 11, 4, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 21, 94, 94, 94, 94, 94, 1, 29, 29, 29, 21, 21, 16, 16, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 10, 10, 94, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 251
number of broken/clashed sets: 89
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497604 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497604
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497604/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497604
Building REAL300025497605
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497605'
/scratch/stefan/7787277/working/building/REAL300025497605 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497605

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497605/0 /scratch/stefan/7787277/working/building/REAL300025497605 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 468)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/468
`/scratch/stefan/7787277/working/3D/468' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1)

`REAL300025497605.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497605.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497605/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497605 none CCOC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [194, 194, 192, 145, 145, 145, 94, 94, 94, 94, 94, 64, 37, 64, 13, 1, 1, 1, 1, 1, 1, 1, 94, 192, 201, 201, 194, 194, 194, 194, 194, 192, 145, 94, 94, 94, 94, 94, 37, 37, 1, 94, 94, 201, 201, 201, 201, 201] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 758
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497605 none CCOC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 5, 1, 5, 10, 10, 10, 21, 21, 21, 21, 21, 40, 40, 70, 100, 201, 201, 201, 201, 201, 21, 1, 1, 1, 8, 8, 8, 8, 8, 5, 10, 21, 21, 21, 21, 21, 70, 70, 201, 21, 21, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 43, 44, 45, 46, 47, 23, 24, 25] set([0, 1, 2, 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: 498
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497605 none CCOC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 16, 94, 94, 94, 94, 94, 1, 14, 21, 21, 17, 17, 17, 17, 17, 14, 5, 1, 1, 1, 1, 1, 9, 10, 94, 1, 1, 21, 21, 21, 21, 21] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47])
total number of confs: 212
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497605 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497605
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497605/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497605
Building REAL300025497606
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497606'
/scratch/stefan/7787277/working/building/REAL300025497606 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497606

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497606/0 /scratch/stefan/7787277/working/building/REAL300025497606 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 469)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/469
`/scratch/stefan/7787277/working/3D/469' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCOCC(F)F)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497606.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497606.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497606/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497606 none O=C(CCOCC(F)F)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 15, 15, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 150, 153, 170, 201, 201, 201, 38, 38, 38, 38, 38, 38, 28, 38, 13, 1, 1, 1, 1, 1, 1, 1, 38, 150, 150, 153, 153, 201, 201, 201, 39, 38, 38, 38, 38, 38, 28, 28, 1, 38, 38] 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])
total number of confs: 773
number of broken/clashed sets: 167
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497606 none O=C(CCOCC(F)F)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 12, 5, 5, 15, 15, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need 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, 12, 19, 33, 41, 41, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 7, 38, 38, 38, 38, 38, 1, 11, 11, 12, 12, 33, 33, 41, 3, 1, 1, 1, 1, 1, 4, 4, 38, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 222
number of broken/clashed sets: 167
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497606 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497606
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497606/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497606
Building REAL300025497607
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497607'
/scratch/stefan/7787277/working/building/REAL300025497607 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497607

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497607/0 /scratch/stefan/7787277/working/building/REAL300025497607 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 470)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/470
`/scratch/stefan/7787277/working/3D/470' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1N=CN=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497607.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497607.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497607/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497607 none O=C(CN1N=CN=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 8, 1, 8, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 18, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 48, 48, 48, 48, 48, 1, 18, 18, 42, 4, 1, 1, 1, 1, 1, 5, 5, 48, 1, 1] 201
rigid atoms, others: [32, 33, 37, 38, 8, 9, 10, 11, 12, 13, 14, 24, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 34, 35, 36])
total number of confs: 171
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497607 none O=C(CN1N=CN=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 8, 1, 8, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 126, 201, 201, 201, 201, 48, 48, 48, 48, 48, 38, 27, 38, 13, 1, 1, 1, 1, 1, 1, 1, 48, 126, 126, 201, 68, 48, 48, 48, 48, 48, 27, 27, 1, 48, 48] 201
rigid atoms, others: [36, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38])
total number of confs: 666
number of broken/clashed sets: 61
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497607 none O=C(CN1N=CN=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 8, 1, 8, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 7, 1, 1, 1, 1, 1, 1, 28, 28, 42, 42, 42, 42, 42, 49, 49, 87, 125, 201, 201, 201, 201, 201, 42, 7, 7, 1, 28, 42, 42, 42, 42, 42, 87, 87, 201, 42, 42] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 27] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 537
number of broken/clashed sets: 61
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497607 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497607
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497607/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497607
Building REAL300025497608
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497608'
/scratch/stefan/7787277/working/building/REAL300025497608 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497608

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497608/0 /scratch/stefan/7787277/working/building/REAL300025497608 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 471)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/471
`/scratch/stefan/7787277/working/3D/471' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(Cl)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497608.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497608.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497608/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497608 none CN1N=CC(Cl)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 42, 117, 117, 117, 117, 117, 1, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 21, 21, 117, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 36, 37, 38])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497608 none CN1N=CC(Cl)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 139, 139, 139, 117, 117, 117, 117, 117, 89, 52, 89, 13, 1, 1, 1, 1, 1, 1, 1, 117, 201, 201, 201, 201, 139, 117, 117, 117, 117, 117, 52, 52, 1, 117, 117] 201
rigid atoms, others: [38, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 544
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497608 none CN1N=CC(Cl)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 16, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 11, 11, 11, 11, 11, 35, 35, 69, 110, 201, 201, 201, 201, 201, 11, 2, 2, 2, 1, 5, 11, 11, 11, 11, 11, 69, 69, 201, 11, 11] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 486
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497608 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497608
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497608/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497608
Building REAL300025497609
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497609'
/scratch/stefan/7787277/working/building/REAL300025497609 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497609

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497609/0 /scratch/stefan/7787277/working/building/REAL300025497609 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 472)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/472
`/scratch/stefan/7787277/working/3D/472' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NC=N1)

`REAL300025497609.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497609.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497609/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497609 none COC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 6, 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, 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, 11, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 56, 147, 147, 147, 147, 147, 1, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 29, 29, 147, 1, 1, 11] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42])
total number of confs: 297
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497609 none COC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 6, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 200, 200, 200, 147, 147, 147, 147, 147, 114, 42, 114, 13, 1, 1, 1, 1, 1, 1, 1, 147, 201, 201, 201, 201, 201, 201, 201, 200, 147, 147, 147, 147, 147, 42, 42, 1, 147, 147, 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])
total number of confs: 612
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497609 none COC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 6, 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, 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, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 31, 31, 81, 125, 201, 201, 201, 201, 201, 11, 1, 1, 1, 2, 2, 2, 1, 4, 11, 11, 11, 11, 11, 81, 81, 201, 11, 11, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 24, 25, 26, 30] set([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])
total number of confs: 523
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497609 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497609
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497609/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497609
Building REAL300025497610
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497610'
/scratch/stefan/7787277/working/building/REAL300025497610 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497610

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497610/0 /scratch/stefan/7787277/working/building/REAL300025497610 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 473)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/473
`/scratch/stefan/7787277/working/3D/473' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2C[NH+]3CCC2CC3)C1)

`REAL300025497610.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497610.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497610/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497610 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2C[NH+]3CCC2CC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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, 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
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 15, 25, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 1, 15, 15, 49, 1, 1, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 52
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 49, 50, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 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: 127
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497610 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2C[NH+]3CCC2CC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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, 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
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [16, 7, 16, 26, 36, 52, 52, 52, 52, 52, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 26, 26, 52, 7, 7, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 52
rigid atoms, others: [16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 49, 50])
total number of confs: 144
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497610 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2C[NH+]3CCC2CC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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, 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
52  conformations in input
total number of sets (complete confs): 52
using faster count positions algorithm for large data
unique positions, atoms: [44, 29, 13, 1, 1, 1, 1, 1, 1, 1, 44, 49, 49, 49, 49, 49, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 49, 29, 29, 1, 49, 49, 49, 49, 49, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 49, 49] 52
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 168
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497610 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497610
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497610/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497610
Building REAL300025497611
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497611'
/scratch/stefan/7787277/working/building/REAL300025497611 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497611

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497611/0 /scratch/stefan/7787277/working/building/REAL300025497611 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 474)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/474
`/scratch/stefan/7787277/working/3D/474' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC[C@@H](C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497611.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497611.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497611/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497611 none CCCC[C@@H](C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 185, 101, 185, 185, 101, 101, 53, 53, 53, 53, 53, 43, 26, 43, 12, 1, 1, 1, 1, 1, 1, 1, 53, 201, 201, 201, 201, 201, 201, 201, 201, 201, 185, 185, 185, 101, 53, 53, 53, 53, 53, 26, 26, 1, 53, 53] 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: 778
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: REAL300025497611 none CCCC[C@@H](C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 5, 5, 7, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [42, 41, 41, 21, 4, 21, 21, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 22, 53, 53, 53, 53, 53, 1, 42, 42, 42, 42, 42, 41, 41, 41, 41, 21, 21, 21, 4, 1, 1, 1, 1, 1, 12, 12, 53, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 273
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497611 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497611
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497611/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497611
Building REAL300025497612
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497612'
/scratch/stefan/7787277/working/building/REAL300025497612 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497612

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497612/0 /scratch/stefan/7787277/working/building/REAL300025497612 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 475)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/475
`/scratch/stefan/7787277/working/3D/475' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497612.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497612.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497612/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497612 none CCC1=CC=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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: [9, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 32, 92, 92, 92, 92, 92, 1, 5, 9, 9, 9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 19, 19, 92, 1, 1, 5] 201
rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45])
total number of confs: 213
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497612 none CCC1=CC=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 108, 108, 108, 108, 108, 108, 108, 108, 92, 92, 92, 92, 92, 74, 37, 74, 13, 1, 1, 1, 1, 1, 1, 1, 92, 108, 201, 201, 201, 201, 201, 108, 108, 108, 92, 92, 92, 92, 92, 37, 37, 1, 92, 92, 108] 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: 900
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497612 none CCC1=CC=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 18, 18, 40, 61, 108, 108, 108, 108, 108, 5, 1, 3, 3, 3, 2, 2, 1, 1, 2, 5, 5, 5, 5, 5, 40, 40, 108, 5, 5, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 45, 26] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 284
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497612 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497612
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497612/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497612
Building REAL300025497613
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497613'
/scratch/stefan/7787277/working/building/REAL300025497613 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497613

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497613/0 /scratch/stefan/7787277/working/building/REAL300025497613 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 476)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/476
`/scratch/stefan/7787277/working/3D/476' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1)

`REAL300025497613.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497613.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497613/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497613 none CC1=C(C)CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 27, 59, 59, 59, 59, 59, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 1, 17, 17, 59, 1, 1, 23, 23, 23, 23] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47, 48, 49, 50])
total number of confs: 185
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497613 none CC1=C(C)CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 75, 75, 75, 59, 59, 59, 59, 59, 53, 36, 53, 13, 1, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 75, 59, 59, 59, 59, 59, 36, 36, 1, 59, 59, 201, 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, 48, 49, 50])
total number of confs: 624
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497613 none CC1=C(C)CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 23, 23, 23, 23, 23, 52, 52, 96, 141, 201, 201, 201, 201, 201, 23, 1, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 8, 23, 23, 23, 23, 23, 96, 96, 201, 23, 23, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 34, 47, 48, 49, 50, 35, 25, 26] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 570
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497613 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497613
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497613/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497613
Building REAL300025497614
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497614'
/scratch/stefan/7787277/working/building/REAL300025497614 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497614

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497614/0 /scratch/stefan/7787277/working/building/REAL300025497614 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 477)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/477
`/scratch/stefan/7787277/working/3D/477' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)CCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497614.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497614.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497614/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497614 none CC(C)(C)CCCCC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens need 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, 201, 201, 201, 159, 180, 60, 60, 60, 35, 35, 35, 35, 35, 33, 21, 33, 10, 1, 1, 1, 1, 1, 1, 1, 35, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 180, 180, 60, 35, 35, 35, 35, 35, 21, 21, 1, 35, 35] 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: 1358
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497614 none CC(C)(C)CCCCC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens 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, 33, 42, 42, 42, 33, 27, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 11, 35, 35, 35, 35, 35, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 42, 27, 27, 5, 1, 1, 1, 1, 1, 6, 6, 35, 1, 1] 201
rigid atoms, others: [16, 15, 10, 11, 12, 13, 46, 45, 48, 49, 14, 54, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52])
total number of confs: 345
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497614 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497614
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497614/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497614
Building REAL300025497615
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497615'
/scratch/stefan/7787277/working/building/REAL300025497615 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497615

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497615/0 /scratch/stefan/7787277/working/building/REAL300025497615 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 478)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/478
`/scratch/stefan/7787277/working/3D/478' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC(CC=C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497615.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497615.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497615/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497615 none C=CCC(CC=C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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: [173, 129, 91, 42, 91, 123, 172, 42, 42, 42, 42, 42, 42, 42, 32, 25, 32, 13, 1, 1, 1, 1, 1, 1, 1, 42, 173, 173, 173, 129, 129, 91, 123, 123, 172, 172, 172, 42, 42, 42, 42, 42, 42, 25, 25, 1, 42, 42] 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])
total number of confs: 1125
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: REAL300025497615 none C=CCC(CC=C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 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: [15, 10, 5, 2, 5, 12, 18, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 11, 42, 42, 42, 42, 42, 1, 15, 15, 15, 10, 10, 5, 12, 12, 18, 18, 18, 2, 1, 1, 1, 1, 1, 8, 8, 42, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 189
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497615 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497615
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497615/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497615
Building REAL300025497616
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497616'
/scratch/stefan/7787277/working/building/REAL300025497616 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497616

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497616/0 /scratch/stefan/7787277/working/building/REAL300025497616 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 479)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/479
`/scratch/stefan/7787277/working/3D/479' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC=CCC1)

`REAL300025497616.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497616.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497616/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497616 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 43, 142, 142, 142, 142, 142, 1, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 19, 19, 142, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 39, 20, 38, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 255
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497616 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 198, 198, 198, 142, 142, 142, 142, 142, 113, 60, 113, 13, 1, 1, 1, 1, 1, 1, 1, 142, 201, 201, 201, 201, 201, 201, 201, 201, 198, 142, 142, 142, 142, 142, 60, 60, 1, 142, 142, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 621
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497616 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 21, 21, 52, 104, 201, 201, 201, 201, 201, 7, 1, 1, 1, 1, 1, 2, 2, 2, 3, 7, 7, 7, 7, 7, 52, 52, 201, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 40, 41, 42, 43, 44, 45, 46, 47, 21, 22, 23, 24, 25] set([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])
total number of confs: 446
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497616 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497616
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497616/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497616
Building REAL300025497617
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497617'
/scratch/stefan/7787277/working/building/REAL300025497617 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497617

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497617/0 /scratch/stefan/7787277/working/building/REAL300025497617 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 480)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/480
`/scratch/stefan/7787277/working/3D/480' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(Cl)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025497617.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497617.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497617/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497617 none CN1C=C(Cl)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 28, 88, 88, 88, 88, 88, 1, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 14, 14, 88, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 180
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497617 none CN1C=C(Cl)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 109, 109, 109, 88, 88, 88, 88, 88, 73, 46, 73, 13, 1, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 201, 201, 109, 88, 88, 88, 88, 88, 46, 46, 1, 88, 88] 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])
total number of confs: 526
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497617 none CN1C=C(Cl)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 33, 33, 59, 103, 201, 201, 201, 201, 201, 11, 1, 2, 2, 2, 1, 5, 11, 11, 11, 11, 11, 59, 59, 201, 11, 11] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 29] set([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])
total number of confs: 450
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497617 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497617
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497617/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497617
Building REAL300025497618
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497618'
/scratch/stefan/7787277/working/building/REAL300025497618 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497618

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497618/0 /scratch/stefan/7787277/working/building/REAL300025497618 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 481)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/481
`/scratch/stefan/7787277/working/3D/481' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CS(=O)(=O)C2)C1)

`REAL300025497618.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497618.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497618/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497618 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CS(=O)(=O)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 14, 11, 11, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 14, 29, 102, 102, 102, 102, 102, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 16, 1, 14, 14, 102, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 1, 1] 201
rigid atoms, others: [32, 1, 39, 40, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38])
total number of confs: 207
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497618 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CS(=O)(=O)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 14, 11, 11, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 16, 38, 78, 111, 201, 201, 201, 201, 201, 16, 16, 16, 16, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 16, 78, 78, 201, 16, 16, 16, 16, 16, 8, 1, 1, 1, 1, 1, 16, 16] 201
rigid atoms, others: [34, 35, 36, 37, 38, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40])
total number of confs: 524
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497618 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CS(=O)(=O)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 14, 11, 11, 5, 5, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [76, 45, 13, 1, 1, 1, 1, 1, 1, 1, 76, 102, 102, 102, 102, 102, 136, 136, 136, 201, 201, 201, 201, 201, 102, 45, 45, 1, 102, 102, 102, 102, 102, 136, 201, 201, 201, 201, 201, 102, 102] 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: 657
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497618 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497618
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497618/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497618
Building REAL300025497619
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497619'
/scratch/stefan/7787277/working/building/REAL300025497619 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497619

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497619/0 /scratch/stefan/7787277/working/building/REAL300025497619 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 482)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/482
`/scratch/stefan/7787277/working/3D/482' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CS1)

`REAL300025497619.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497619.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497619/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497619 none CC1=C(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CS1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 6, 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: [24, 24, 24, 24, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 31, 64, 64, 64, 64, 64, 1, 24, 24, 24, 24, 24, 24, 24, 24, 5, 1, 1, 1, 1, 1, 19, 19, 64, 1, 1, 24] 201
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 176
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497619 none CC1=C(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CS1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 6, 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, 91, 91, 91, 64, 64, 64, 64, 64, 53, 36, 53, 13, 1, 1, 1, 1, 1, 1, 1, 64, 201, 201, 201, 201, 201, 201, 201, 201, 91, 64, 64, 64, 64, 64, 36, 36, 1, 64, 64, 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])
total number of confs: 468
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497619 none CC1=C(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CS1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 14, 7, 7, 7, 7, 7, 7, 6, 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, 8, 8, 8, 24, 24, 24, 24, 24, 50, 50, 93, 135, 201, 201, 201, 201, 201, 24, 1, 1, 2, 2, 2, 2, 2, 2, 8, 24, 24, 24, 24, 24, 93, 93, 201, 24, 24, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 545
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497619 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497619
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497619/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497619
Building REAL300025497620
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497620'
/scratch/stefan/7787277/working/building/REAL300025497620 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497620

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497620/0 /scratch/stefan/7787277/working/building/REAL300025497620 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 483)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/483
`/scratch/stefan/7787277/working/3D/483' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497620.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497620.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497620/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497620 none CCC(C)(C)CC(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 65, 65, 65, 41, 41, 41, 41, 41, 39, 28, 39, 13, 1, 1, 1, 1, 1, 1, 1, 41, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 65, 41, 41, 41, 41, 41, 28, 28, 1, 41, 41] 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])
total number of confs: 890
number of broken/clashed sets: 41
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497620 none CCC(C)(C)CC(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 10, 32, 32, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 10, 41, 41, 41, 41, 41, 1, 41, 41, 41, 41, 41, 32, 32, 32, 32, 32, 32, 10, 10, 5, 1, 1, 1, 1, 1, 6, 6, 41, 1, 1] 201
rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 238
number of broken/clashed sets: 41
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497620 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497620
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497620/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497620
Building REAL300025497621
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497621'
/scratch/stefan/7787277/working/building/REAL300025497621 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497621

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497621/0 /scratch/stefan/7787277/working/building/REAL300025497621 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 484)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/484
`/scratch/stefan/7787277/working/3D/484' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(C)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497621.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497621.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497621/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497621 none CCCC(C)CCCC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 133, 201, 127, 113, 55, 55, 55, 55, 55, 55, 55, 55, 46, 26, 46, 12, 1, 1, 1, 1, 1, 1, 1, 55, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 133, 133, 133, 113, 113, 55, 55, 55, 55, 55, 55, 26, 26, 1, 55, 55] 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: 984
number of broken/clashed sets: 122
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497621 none CCCC(C)CCCC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens 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, 35, 18, 35, 15, 10, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 12, 55, 55, 55, 55, 55, 1, 44, 44, 44, 44, 44, 44, 44, 35, 35, 35, 35, 18, 18, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 6, 6, 55, 1, 1] 201
rigid atoms, others: [16, 15, 10, 11, 12, 13, 46, 45, 48, 49, 14, 54, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52])
total number of confs: 328
number of broken/clashed sets: 122
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497621 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497621
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497621/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497621
Building REAL300025497622
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497622'
/scratch/stefan/7787277/working/building/REAL300025497622 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497622

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497622/0 /scratch/stefan/7787277/working/building/REAL300025497622 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 485)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/485
`/scratch/stefan/7787277/working/3D/485' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)CCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497622.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497622.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497622/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497622 none CCC(C)CCCCC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 105, 201, 119, 105, 119, 44, 44, 44, 44, 44, 44, 44, 44, 40, 26, 40, 13, 1, 1, 1, 1, 1, 1, 1, 44, 201, 201, 201, 201, 201, 201, 201, 201, 201, 119, 119, 119, 119, 119, 119, 119, 119, 44, 44, 44, 44, 44, 44, 26, 26, 1, 44, 44] 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: 1087
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: REAL300025497622 none CCC(C)CCCCC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens 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, 24, 13, 12, 10, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 44, 44, 44, 44, 44, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 13, 13, 13, 13, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 5, 5, 44, 1, 1] 201
rigid atoms, others: [16, 15, 10, 11, 12, 13, 46, 45, 48, 49, 14, 54, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52])
total number of confs: 190
number of broken/clashed sets: 63
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497622 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497622
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497622/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497622
Building REAL300025497623
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497623'
/scratch/stefan/7787277/working/building/REAL300025497623 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497623

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497623/0 /scratch/stefan/7787277/working/building/REAL300025497623 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 486)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/486
`/scratch/stefan/7787277/working/3D/486' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497623.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497623.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497623/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497623 none CC(C)C(C)(C)C(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [18, 18, 18, 10, 18, 18, 10, 10, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 1, 1, 1, 1, 1, 1, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 9, 9, 9, 9, 9, 9, 9, 1, 9, 9] 18
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])
total number of confs: 72
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: REAL300025497623 none CC(C)C(C)(C)C(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
18  conformations in input
total number of sets (complete confs): 18
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 8, 5, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 9, 9, 9, 9, 9, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 7, 7, 9, 1, 1] 18
rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 55
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497623 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497623
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497623/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497623
Building REAL300025497624
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497624'
/scratch/stefan/7787277/working/building/REAL300025497624 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497624

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497624/0 /scratch/stefan/7787277/working/building/REAL300025497624 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 487)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/487
`/scratch/stefan/7787277/working/3D/487' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(Cl)C(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497624.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497624.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497624/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497624 none C=C(Cl)C(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 16, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 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, 9, 12, 12, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 12, 12, 12, 12, 12, 9, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6] 12
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43])
total number of confs: 38
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: REAL300025497624 none C=C(Cl)C(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 16, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [10, 8, 10, 6, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 6, 6, 6, 6, 6, 1, 10, 10, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 5, 5, 6, 1, 1] 12
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 49
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497624 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497624
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497624/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497624
Building REAL300025497625
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497625'
/scratch/stefan/7787277/working/building/REAL300025497625 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497625

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497625/0 /scratch/stefan/7787277/working/building/REAL300025497625 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 488)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/488
`/scratch/stefan/7787277/working/3D/488' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)N1N=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497625.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497625.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497625/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497625 none CC(C)N1N=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 13, 26, 13, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 28, 118, 118, 118, 118, 118, 1, 26, 26, 26, 26, 26, 26, 26, 13, 13, 5, 1, 1, 1, 1, 1, 15, 15, 118, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 279
number of broken/clashed sets: 46
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497625 none CC(C)N1N=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
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, 157, 157, 157, 118, 118, 118, 118, 118, 72, 30, 72, 13, 1, 1, 1, 1, 1, 1, 1, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 157, 118, 118, 118, 118, 118, 30, 30, 1, 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])
total number of confs: 537
number of broken/clashed sets: 46
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497625 none CC(C)N1N=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 33, 33, 66, 101, 201, 201, 201, 201, 201, 13, 4, 4, 4, 4, 4, 4, 4, 1, 1, 5, 13, 13, 13, 13, 13, 66, 66, 201, 13, 13] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 35] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 482
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497625 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497625
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497625/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497625
Building REAL300025497626
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497626'
/scratch/stefan/7787277/working/building/REAL300025497626 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497626

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497626/0 /scratch/stefan/7787277/working/building/REAL300025497626 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 489)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/489
`/scratch/stefan/7787277/working/3D/489' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NN(C(F)F)C=C2)C1)

`REAL300025497626.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497626.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497626/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497626 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NN(C(F)F)C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 8, 8, 5, 15, 15, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 36, 36, 8, 8, 1, 13, 13, 121, 1, 1, 1, 1, 1, 5, 36, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 10, 11, 12, 13, 14, 15, 39, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38])
total number of confs: 294
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497626 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NN(C(F)F)C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 8, 8, 5, 15, 15, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 45, 72, 201, 201, 201, 201, 201, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 11, 11, 1, 1, 8, 45, 45, 201, 8, 8, 8, 8, 8, 3, 11, 1, 1, 8, 8] 201
rigid atoms, others: [37, 38, 16, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40])
total number of confs: 418
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497626 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NN(C(F)F)C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 8, 8, 5, 15, 15, 1, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 38, 13, 1, 1, 1, 1, 1, 1, 1, 82, 121, 121, 121, 121, 121, 198, 198, 198, 201, 201, 201, 201, 201, 201, 201, 121, 38, 38, 1, 121, 121, 121, 121, 121, 198, 201, 201, 201, 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])
total number of confs: 623
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497626 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497626
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497626/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497626
Building REAL300025497627
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497627'
/scratch/stefan/7787277/working/building/REAL300025497627 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497627

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497627/0 /scratch/stefan/7787277/working/building/REAL300025497627 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 490)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/490
`/scratch/stefan/7787277/working/3D/490' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NN2C(F)F)C1)

`REAL300025497627.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497627.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497627/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497627 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NN2C(F)F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 28, 28, 1, 10, 10, 95, 1, 1, 1, 1, 1, 5, 12, 12, 28, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 10, 11, 12, 13, 14, 15, 39, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38])
total number of confs: 231
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497627 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NN2C(F)F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 12, 26, 51, 77, 201, 201, 201, 201, 201, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 5, 5, 12, 51, 51, 201, 12, 12, 12, 12, 12, 4, 1, 1, 5, 12, 12] 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: 440
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497627 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NN2C(F)F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'F', 'F', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 15, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 36, 13, 1, 1, 1, 1, 1, 1, 1, 64, 95, 95, 95, 95, 95, 150, 150, 150, 201, 201, 201, 201, 201, 201, 201, 95, 36, 36, 1, 95, 95, 95, 95, 95, 150, 201, 201, 201, 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])
total number of confs: 565
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497627 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497627
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497627/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497627
Building REAL300025497628
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497628'
/scratch/stefan/7787277/working/building/REAL300025497628 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497628

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497628/0 /scratch/stefan/7787277/working/building/REAL300025497628 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 491)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/491
`/scratch/stefan/7787277/working/3D/491' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(C)(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497628.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497628.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497628/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497628 none C=CC(C)(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 175, 201, 201, 101, 101, 101, 71, 71, 71, 71, 71, 56, 28, 56, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 101, 71, 71, 71, 71, 71, 28, 28, 1, 71, 71] 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])
total number of confs: 914
number of broken/clashed sets: 81
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497628 none C=CC(C)(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [25, 18, 10, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 19, 71, 71, 71, 71, 71, 1, 25, 25, 25, 18, 18, 18, 18, 18, 18, 10, 10, 5, 1, 1, 1, 1, 1, 10, 10, 71, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 217
number of broken/clashed sets: 81
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497628 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497628
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497628/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497628
Building REAL300025497629
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497629'
/scratch/stefan/7787277/working/building/REAL300025497629 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497629

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497629/0 /scratch/stefan/7787277/working/building/REAL300025497629 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 492)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/492
`/scratch/stefan/7787277/working/3D/492' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC(C)=N1)

`REAL300025497629.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497629.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497629/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497629 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 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: [9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 34, 115, 115, 115, 115, 115, 1, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 17, 17, 115, 1, 1, 9, 9, 9, 9] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45])
total number of confs: 214
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497629 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 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, 138, 138, 138, 115, 115, 115, 115, 115, 96, 50, 96, 13, 1, 1, 1, 1, 1, 1, 1, 115, 201, 201, 201, 201, 201, 201, 201, 201, 138, 115, 115, 115, 115, 115, 50, 50, 1, 115, 115, 201, 201, 201, 201] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45])
total number of confs: 556
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497629 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 5, 8, 7, 7, 7, 7, 6, 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, 3, 3, 3, 9, 9, 9, 9, 9, 32, 32, 61, 101, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 2, 2, 2, 1, 3, 9, 9, 9, 9, 9, 61, 61, 201, 9, 9, 1, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 42, 23, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45])
total number of confs: 452
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497629 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497629
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497629/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497629
Building REAL300025497630
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497630'
/scratch/stefan/7787277/working/building/REAL300025497630 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497630

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497630/0 /scratch/stefan/7787277/working/building/REAL300025497630 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 493)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/493
`/scratch/stefan/7787277/working/3D/493' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1N=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497630.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497630.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497630/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497630 none O=C(CN1N=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 8, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 24, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 24, 89, 89, 89, 89, 89, 1, 24, 24, 39, 39, 5, 1, 1, 1, 1, 1, 13, 13, 89, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 39, 8, 9, 10, 11, 12, 13, 14, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 257
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497630 none O=C(CN1N=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 8, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 200, 201, 201, 201, 201, 89, 89, 89, 89, 89, 56, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 89, 200, 200, 201, 201, 125, 89, 89, 89, 89, 89, 29, 29, 1, 89, 89] 201
rigid atoms, others: [37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 763
number of broken/clashed sets: 60
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497630 none O=C(CN1N=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 8, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 32, 32, 32, 32, 32, 41, 41, 85, 133, 201, 201, 201, 201, 201, 32, 5, 5, 1, 1, 20, 32, 32, 32, 32, 32, 85, 85, 201, 32, 32] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 528
number of broken/clashed sets: 79
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497630 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497630
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497630/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497630
Building REAL300025497631
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497631'
/scratch/stefan/7787277/working/building/REAL300025497631 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497631

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497631/0 /scratch/stefan/7787277/working/building/REAL300025497631 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 494)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/494
`/scratch/stefan/7787277/working/3D/494' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1)

`REAL300025497631.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497631.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497631/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497631 none CC1=CC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 37, 90, 90, 90, 90, 90, 1, 21, 21, 21, 21, 21, 21, 21, 21, 4, 1, 1, 1, 1, 1, 22, 22, 90, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 212
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497631 none CC1=CC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 122, 122, 122, 90, 90, 90, 90, 90, 73, 37, 73, 13, 1, 1, 1, 1, 1, 1, 1, 90, 201, 201, 201, 201, 201, 201, 201, 201, 122, 90, 90, 90, 90, 90, 37, 37, 1, 90, 90] 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])
total number of confs: 531
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497631 none CC1=CC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 21, 21, 21, 21, 21, 48, 48, 105, 139, 201, 201, 201, 201, 201, 21, 1, 2, 2, 2, 1, 2, 2, 2, 9, 21, 21, 21, 21, 21, 105, 105, 201, 21, 21] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 593
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497631 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497631
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497631/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497631
Building REAL300025497632
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497632'
/scratch/stefan/7787277/working/building/REAL300025497632 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497632

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497632/0 /scratch/stefan/7787277/working/building/REAL300025497632 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 495)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/495
`/scratch/stefan/7787277/working/3D/495' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CNN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497632.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497632.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497632/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497632 none O=C(CCC1=CNN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 19, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 25, 91, 91, 91, 91, 91, 1, 19, 19, 27, 27, 27, 27, 27, 5, 1, 1, 1, 1, 1, 15, 15, 91, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 257
number of broken/clashed sets: 70
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497632 none O=C(CCC1=CNN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [124, 124, 124, 190, 201, 201, 201, 201, 201, 91, 91, 91, 91, 91, 60, 29, 60, 13, 1, 1, 1, 1, 1, 1, 1, 91, 190, 190, 201, 201, 201, 201, 201, 124, 91, 91, 91, 91, 91, 29, 29, 1, 91, 91] 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])
total number of confs: 755
number of broken/clashed sets: 70
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497632 none O=C(CCC1=CNN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 5, 2, 1, 1, 1, 1, 1, 1, 20, 20, 35, 35, 35, 35, 35, 41, 41, 81, 119, 201, 201, 201, 201, 201, 35, 5, 5, 2, 2, 1, 1, 1, 20, 35, 35, 35, 35, 35, 81, 81, 201, 35, 35] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 518
number of broken/clashed sets: 74
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497632 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497632
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497632/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497632
Building REAL300025497633
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497633'
/scratch/stefan/7787277/working/building/REAL300025497633 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497633

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497633/0 /scratch/stefan/7787277/working/building/REAL300025497633 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 496)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/496
`/scratch/stefan/7787277/working/3D/496' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1=CNC=N1)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497633.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497633.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497633/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497633 none CC(CC1=CNC=N1)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 5, 14, 18, 29, 29, 29, 29, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 17, 73, 73, 73, 73, 73, 1, 14, 14, 14, 14, 18, 18, 29, 29, 29, 5, 1, 1, 1, 1, 1, 8, 8, 73, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 197
number of broken/clashed sets: 75
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497633 none CC(CC1=CNC=N1)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens 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, 125, 197, 201, 201, 201, 201, 201, 125, 125, 73, 73, 73, 73, 73, 58, 31, 58, 13, 1, 1, 1, 1, 1, 1, 1, 73, 197, 197, 197, 197, 201, 201, 201, 201, 201, 125, 73, 73, 73, 73, 73, 31, 31, 1, 73, 73] 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])
total number of confs: 794
number of broken/clashed sets: 75
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497633 none CC(CC1=CNC=N1)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 6, 1, 1, 1, 1, 1, 1, 8, 17, 17, 17, 29, 29, 29, 29, 29, 42, 42, 83, 123, 201, 201, 201, 201, 201, 29, 8, 8, 8, 8, 6, 6, 1, 1, 1, 17, 29, 29, 29, 29, 29, 83, 83, 201, 29, 29] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 35] 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, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 546
number of broken/clashed sets: 75
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497633 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497633/1 /scratch/stefan/7787277/working/building/REAL300025497633 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 497)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/497
`/scratch/stefan/7787277/working/3D/497' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1=CN=CN1)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497633.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497633.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497633/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497633 none CC(CC1=CN=CN1)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens 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, 18, 24, 25, 25, 25, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 32, 107, 107, 107, 107, 107, 1, 18, 18, 18, 18, 24, 24, 25, 25, 25, 5, 1, 1, 1, 1, 1, 17, 17, 107, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 282
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497633 none CC(CC1=CN=CN1)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens 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, 133, 197, 200, 201, 201, 201, 201, 133, 133, 107, 107, 107, 107, 107, 62, 31, 62, 13, 1, 1, 1, 1, 1, 1, 1, 107, 197, 197, 197, 197, 200, 200, 201, 201, 201, 133, 107, 107, 107, 107, 107, 31, 31, 1, 107, 107] 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])
total number of confs: 730
number of broken/clashed sets: 52
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497633 none CC(CC1=CN=CN1)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 8, 1, 8, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 25, 25, 25, 25, 25, 46, 46, 86, 125, 201, 201, 201, 201, 201, 25, 5, 5, 5, 5, 3, 3, 1, 1, 1, 11, 25, 25, 25, 25, 25, 86, 86, 201, 25, 25] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 35] 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, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 540
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497633 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497633
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497633/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497633/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497633
Building REAL300025497634
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497634'
/scratch/stefan/7787277/working/building/REAL300025497634 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497634

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497634/0 /scratch/stefan/7787277/working/building/REAL300025497634 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 498)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/498
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2CC2)C1)

`REAL300025497634.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497634.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497634/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025497634 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 8, 12, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 4, 4, 4, 20, 20, 20, 20, 20, 41, 41, 1, 8, 8, 62, 1, 1, 1, 1, 1, 4, 20, 20, 41, 41, 41, 41, 41, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 44, 10, 11, 12, 13, 14, 15, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 207
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.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: REAL300025497634 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [66, 41, 66, 93, 120, 201, 201, 201, 201, 201, 41, 41, 41, 41, 26, 26, 5, 26, 5, 5, 5, 1, 5, 1, 1, 1, 41, 93, 93, 201, 41, 41, 41, 41, 41, 26, 5, 5, 1, 1, 1, 1, 1, 41, 41] 201
rigid atoms, others: [38, 39, 40, 41, 42, 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, 43, 44])
total number of confs: 544
number of broken/clashed sets: 10
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497634 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 60, 81, 198, 198, 198, 198, 198, 20, 20, 20, 20, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 20, 60, 60, 198, 20, 20, 20, 20, 20, 11, 1, 1, 5, 5, 5, 5, 5, 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, 41, 42, 43, 44])
total number of confs: 455
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497634 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 32, 12, 1, 1, 1, 1, 1, 1, 1, 46, 62, 62, 62, 62, 62, 86, 86, 86, 198, 198, 198, 198, 198, 201, 201, 62, 32, 32, 1, 62, 62, 62, 62, 62, 86, 198, 198, 201, 201, 201, 201, 201, 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])
total number of confs: 629
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497634 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497634
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497634/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497634
Building REAL300025497635
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497635'
/scratch/stefan/7787277/working/building/REAL300025497635 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497635

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497635/0 /scratch/stefan/7787277/working/building/REAL300025497635 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 499)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/499
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2CCC2)C1)

`REAL300025497635.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497635.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497635/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025497635 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 6, 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, 18, 32, 95, 95, 95, 95, 95, 1, 1, 1, 1, 1, 1, 5, 5, 5, 24, 24, 24, 24, 24, 29, 29, 29, 1, 18, 18, 95, 1, 1, 1, 1, 1, 5, 24, 24, 29, 29, 29, 29, 29, 29, 29, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 47, 10, 11, 12, 13, 14, 15, 46, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 256
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.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: REAL300025497635 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 6, 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: [57, 29, 57, 87, 125, 201, 201, 201, 201, 201, 29, 29, 29, 29, 16, 16, 3, 16, 3, 3, 3, 1, 3, 1, 1, 1, 1, 29, 87, 87, 201, 29, 29, 29, 29, 29, 16, 3, 3, 1, 1, 1, 1, 1, 1, 1, 29, 29] 201
rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 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, 46, 47])
total number of confs: 528
number of broken/clashed sets: 14
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497635 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 6, 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: [52, 24, 52, 82, 121, 200, 200, 200, 200, 200, 24, 24, 24, 24, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 3, 3, 3, 24, 82, 82, 200, 24, 24, 24, 24, 24, 11, 1, 1, 3, 3, 3, 3, 3, 3, 3, 24, 24] 201
rigid atoms, others: [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, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 525
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497635 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 7, 6, 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: [75, 41, 13, 1, 1, 1, 1, 1, 1, 1, 75, 95, 95, 95, 95, 95, 110, 110, 110, 200, 200, 200, 200, 200, 201, 201, 201, 95, 41, 41, 1, 95, 95, 95, 95, 95, 110, 200, 200, 201, 201, 201, 201, 201, 201, 201, 95, 95] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 645
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497635 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497635
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497635/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497635
Building REAL300025497636
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497636'
/scratch/stefan/7787277/working/building/REAL300025497636 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497636

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497636/0 /scratch/stefan/7787277/working/building/REAL300025497636 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 500)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/500
`/scratch/stefan/7787277/working/3D/500' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)[C@@H]1OCC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497636.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497636.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497636/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497636 none C=C(C)[C@@H]1OCC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 44, 132, 132, 132, 132, 132, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 1, 23, 23, 132, 1, 1] 201
rigid atoms, others: [48, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 253
number of broken/clashed sets: 41
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497636 none C=C(C)[C@@H]1OCC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
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, 192, 201, 192, 192, 131, 131, 131, 131, 131, 79, 30, 79, 12, 1, 1, 1, 1, 1, 1, 1, 131, 201, 201, 201, 201, 201, 201, 201, 201, 201, 192, 131, 132, 132, 132, 131, 30, 30, 1, 131, 131] 201
rigid atoms, others: [46, 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, 47, 48])
total number of confs: 604
number of broken/clashed sets: 41
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497636 none C=C(C)[C@@H]1OCC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 27, 27, 69, 114, 201, 201, 201, 201, 201, 7, 3, 3, 3, 3, 3, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 69, 69, 201, 7, 7] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 35, 36, 37] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 493
number of broken/clashed sets: 41
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497636 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497636
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497636/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497636
Building REAL300025497637
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497637'
/scratch/stefan/7787277/working/building/REAL300025497637 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497637

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497637/0 /scratch/stefan/7787277/working/building/REAL300025497637 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 501)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/501
`/scratch/stefan/7787277/working/3D/501' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=NN1C)

`REAL300025497637.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497637.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497637/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497637 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [198, 126, 126, 126, 97, 97, 97, 97, 97, 53, 29, 53, 13, 1, 1, 1, 1, 1, 1, 1, 97, 198, 201, 201, 201, 201, 201, 198, 198, 198, 198, 126, 97, 97, 97, 97, 97, 29, 29, 1, 97, 97, 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])
total number of confs: 738
number of broken/clashed sets: 55
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497637 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 14, 27, 27, 27, 27, 27, 59, 59, 95, 134, 201, 201, 201, 201, 201, 27, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 27, 27, 27, 27, 27, 95, 95, 201, 27, 27, 1, 1, 2, 2, 2] 201
rigid atoms, others: [1, 42, 43, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46])
total number of confs: 560
number of broken/clashed sets: 55
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497637 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 8, 8, 5, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 24, 97, 97, 97, 97, 97, 1, 18, 27, 27, 27, 27, 27, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 15, 15, 97, 1, 1, 27, 27, 27, 27, 27] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 40, 20, 41, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46])
total number of confs: 242
number of broken/clashed sets: 55
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497637 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497637
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497637/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497637
Building REAL300025497638
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497638'
/scratch/stefan/7787277/working/building/REAL300025497638 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497638

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497638/0 /scratch/stefan/7787277/working/building/REAL300025497638 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 502)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/502
`/scratch/stefan/7787277/working/3D/502' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NSC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497638.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497638.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497638/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497638 none COC1=NSC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 42, 102, 102, 102, 102, 102, 1, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 24, 24, 102, 1, 1, 16] 201
rigid atoms, others: [32, 33, 34, 38, 39, 8, 9, 10, 11, 12, 13, 14, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37, 40])
total number of confs: 234
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497638 none COC1=NSC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 144, 144, 144, 102, 102, 102, 102, 102, 78, 41, 78, 13, 1, 1, 1, 1, 1, 1, 1, 102, 201, 201, 201, 201, 144, 102, 102, 102, 102, 102, 41, 41, 1, 102, 102, 201] 201
rigid atoms, others: [37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 572
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497638 none COC1=NSC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 14, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 16, 16, 16, 16, 16, 46, 46, 95, 130, 201, 201, 201, 201, 201, 16, 1, 2, 2, 2, 7, 16, 16, 16, 16, 16, 95, 95, 201, 16, 16, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 40, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 557
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497638 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497638
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497638/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497638
Building REAL300025497639
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497639'
/scratch/stefan/7787277/working/building/REAL300025497639 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497639

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497639/0 /scratch/stefan/7787277/working/building/REAL300025497639 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 503)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/503
`/scratch/stefan/7787277/working/3D/503' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN3CCCC3=N2)C1)

`REAL300025497639.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497639.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497639/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497639 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN3CCCC3=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 1, 8, 5, 7, 7, 6, 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]
0  hydrogens 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, 35, 59, 148, 148, 148, 148, 148, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 1, 35, 35, 148, 1, 1, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 44, 10, 11, 12, 13, 14, 15, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 312
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497639 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN3CCCC3=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 1, 8, 5, 7, 7, 6, 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]
0  hydrogens 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, 84, 121, 201, 201, 201, 201, 201, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 84, 84, 201, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 16, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44])
total number of confs: 519
number of broken/clashed sets: 31
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497639 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN3CCCC3=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 1, 8, 5, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [114, 44, 13, 1, 1, 1, 1, 1, 1, 1, 114, 148, 148, 148, 148, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 148, 44, 44, 1, 148, 148, 148, 148, 148, 201, 201, 201, 201, 201, 201, 201, 201, 148, 148] 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: 613
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497639 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497639
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497639/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497639
Building REAL300025497640
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497640'
/scratch/stefan/7787277/working/building/REAL300025497640 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497640

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497640/0 /scratch/stefan/7787277/working/building/REAL300025497640 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 504)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/504
`/scratch/stefan/7787277/working/3D/504' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1[C@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@@H+]1C)

`REAL300025497640.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497640.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497640/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497640 none C[C@@H]1[C@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 5, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 14, 20, 20, 20, 20, 20, 1, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 10, 10, 20, 1, 1, 9, 9, 9, 9, 9, 9, 9] 25
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 75
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497640 none C[C@@H]1[C@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 20, 20, 20, 20, 20, 18, 17, 18, 11, 1, 1, 1, 1, 1, 1, 1, 20, 25, 25, 25, 25, 25, 25, 25, 25, 25, 20, 20, 20, 20, 20, 17, 17, 1, 20, 20, 25, 25, 25, 25, 25, 25, 25] 25
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 73
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497640 none C[C@@H]1[C@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
25  conformations in input
total number of sets (complete confs): 25
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 14, 14, 20, 21, 25, 25, 25, 25, 25, 9, 1, 1, 1, 1, 1, 2, 2, 2, 4, 9, 9, 9, 9, 9, 20, 20, 25, 9, 9, 1, 1, 1, 1, 2, 2, 2] 25
rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 44, 45, 46, 24, 25, 26, 27, 28] set([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, 47, 48, 49])
total number of confs: 91
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497640 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497640/1 /scratch/stefan/7787277/working/building/REAL300025497640 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 505)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/505
`/scratch/stefan/7787277/working/3D/505' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1[C@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@H+]1C)

`REAL300025497640.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497640.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497640/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497640 none C[C@@H]1[C@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 5, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 12, 15, 15, 15, 15, 15, 1, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 8, 8, 15, 1, 1, 9, 9, 9, 9, 9, 9, 9] 17
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 63
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497640 none C[C@@H]1[C@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 15, 15, 15, 15, 15, 15, 14, 15, 10, 1, 1, 1, 1, 1, 1, 1, 15, 17, 17, 17, 17, 17, 17, 17, 17, 17, 15, 15, 15, 15, 15, 14, 14, 1, 15, 15, 17, 17, 17, 17, 17, 17, 17] 17
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 47
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497640 none C[C@@H]1[C@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 14, 14, 16, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 2, 2, 2, 5, 9, 9, 9, 9, 9, 16, 16, 17, 9, 9, 1, 1, 1, 1, 2, 2, 2] 17
rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 44, 45, 46, 24, 25, 26, 27, 28] set([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, 47, 48, 49])
total number of confs: 69
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497640 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497640
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497640/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497640/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497640
Building REAL300025497641
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497641'
/scratch/stefan/7787277/working/building/REAL300025497641 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497641

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497641/0 /scratch/stefan/7787277/working/building/REAL300025497641 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 506)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/506
`/scratch/stefan/7787277/working/3D/506' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497641.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497641.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497641/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497641 none CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1C=CCN(C(=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', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 19, 19, 19, 4, 19, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 44, 44, 44, 44, 44, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 19, 19, 4, 1, 1, 1, 1, 1, 5, 5, 44, 1, 1] 201
rigid atoms, others: [45, 44, 43, 12, 13, 14, 15, 16, 17, 18, 51, 52, 46, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 199
number of broken/clashed sets: 183
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497641 none CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1C=CCN(C(=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', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 159, 159, 159, 159, 70, 159, 70, 70, 44, 44, 44, 44, 44, 41, 28, 41, 13, 1, 1, 1, 1, 1, 1, 1, 44, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 159, 159, 70, 44, 44, 44, 44, 44, 28, 28, 1, 44, 44] 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, 51, 52])
total number of confs: 733
number of broken/clashed sets: 183
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497641 none CC(C)(C)C[C@@H]1C[C@H]1C(=O)NC1C=CCN(C(=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', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 19, 19, 19, 19, 19, 21, 21, 49, 78, 159, 159, 159, 159, 159, 19, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 11, 19, 19, 19, 19, 19, 49, 49, 159, 19, 19] 201
rigid atoms, others: [4, 5, 6, 7, 8, 41, 10, 40, 9] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 381
number of broken/clashed sets: 183
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497641 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497641
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497641/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497641
Building REAL300025497642
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497642'
/scratch/stefan/7787277/working/building/REAL300025497642 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497642

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497642/0 /scratch/stefan/7787277/working/building/REAL300025497642 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 507)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/507
`/scratch/stefan/7787277/working/3D/507' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@@H+]1C)

`REAL300025497642.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497642.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497642/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497642 none CC[C@@H]1[C@@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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: [4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 5, 5, 5, 5, 5, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 5, 1, 1, 4, 4, 4, 4, 4, 4, 4] 5
rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 19
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497642 none CC[C@@H]1[C@@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 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, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5] 5
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 11
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497642 none CC[C@@H]1[C@@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
5  conformations in input
total number of sets (complete confs): 5
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 4, 4, 4, 4, 4, 5, 5, 5, 4, 4, 1, 1, 1, 1, 2, 2, 2] 5
rigid atoms, others: [1, 2, 3, 4, 5, 6, 46, 47, 48, 49, 25, 26, 27, 28, 29] set([0, 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: 27
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497642 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497642/1 /scratch/stefan/7787277/working/building/REAL300025497642 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 508)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/508
`/scratch/stefan/7787277/working/3D/508' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1[C@@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@H+]1C)

`REAL300025497642.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497642.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497642/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497642 none CC[C@@H]1[C@@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 4, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 9, 11, 11, 11, 11, 11, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 7, 7, 11, 1, 1, 6, 6, 6, 6, 6, 6, 6] 11
rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 49
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497642 none CC[C@@H]1[C@@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 9, 10, 7, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11] 11
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 26
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497642 none CC[C@@H]1[C@@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC[N@H+]1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 7, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 9, 6, 5, 7, 7, 7, 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, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 4, 4, 4, 6, 6, 6, 6, 6, 7, 7, 9, 10, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 6, 6, 6, 6, 6, 9, 9, 11, 6, 6, 1, 1, 1, 1, 2, 2, 2] 11
rigid atoms, others: [1, 2, 3, 4, 5, 6, 46, 47, 48, 49, 25, 26, 27, 28, 29] set([0, 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: 49
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497642 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497642
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497642/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497642/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497642
Building REAL300025497643
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497643'
/scratch/stefan/7787277/working/building/REAL300025497643 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497643

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497643/0 /scratch/stefan/7787277/working/building/REAL300025497643 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 509)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/509
`/scratch/stefan/7787277/working/3D/509' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@@H]3C=C[C@H]2CC3)C1)

`REAL300025497643.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497643.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497643/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497643 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@@H]3C=C[C@H]2CC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 5, 7, 5, 5, 5, 7, 7, 6, 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, 7]
0  hydrogens 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, 14, 28, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 1, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 15, 15, 103, 1, 1, 1, 1, 1, 4, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1] 201
rigid atoms, others: [1, 34, 35, 36, 37, 33, 10, 11, 12, 13, 14, 15, 48, 47, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 219
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497643 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@@H]3C=C[C@H]2CC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 5, 7, 5, 5, 5, 7, 7, 6, 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, 7]
0  hydrogens 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, 21, 39, 74, 114, 201, 201, 201, 201, 201, 21, 21, 21, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 74, 74, 201, 21, 21, 21, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 201
rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 48])
total number of confs: 496
number of broken/clashed sets: 36
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497643 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@@H]3C=C[C@H]2CC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 5, 7, 5, 5, 5, 7, 7, 6, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 42, 12, 1, 1, 1, 1, 1, 1, 1, 72, 102, 102, 102, 103, 103, 151, 151, 151, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 102, 42, 42, 1, 103, 103, 103, 103, 103, 151, 201, 201, 201, 201, 201, 201, 201, 201, 103, 103] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 651
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497643 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497643
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497643/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497643
Building REAL300025497644
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497644'
/scratch/stefan/7787277/working/building/REAL300025497644 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497644

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497644/0 /scratch/stefan/7787277/working/building/REAL300025497644 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 510)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/510
`/scratch/stefan/7787277/working/3D/510' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025497644.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497644.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497644/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497644 none CCN1C=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [27, 13, 13, 13, 13, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 51, 51, 51, 51, 51, 1, 13, 27, 27, 27, 27, 27, 13, 13, 12, 12, 4, 1, 1, 1, 1, 1, 5, 5, 51, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 191
number of broken/clashed sets: 80
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497644 none CCN1C=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 130, 130, 130, 130, 130, 70, 70, 70, 51, 51, 51, 51, 51, 46, 28, 46, 13, 1, 1, 1, 1, 1, 1, 1, 51, 130, 201, 201, 201, 201, 201, 130, 130, 130, 130, 70, 51, 51, 51, 51, 51, 28, 28, 1, 51, 51] 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])
total number of confs: 970
number of broken/clashed sets: 80
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497644 none CCN1C=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [5, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 13, 13, 13, 13, 13, 18, 18, 36, 62, 130, 130, 130, 130, 130, 13, 1, 5, 5, 5, 5, 5, 1, 1, 4, 4, 8, 13, 13, 13, 13, 13, 36, 36, 130, 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: 313
number of broken/clashed sets: 80
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497644 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497644
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497644/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497644
Building REAL300025497645
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497645'
/scratch/stefan/7787277/working/building/REAL300025497645 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497645

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497645/0 /scratch/stefan/7787277/working/building/REAL300025497645 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 511)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/511
`/scratch/stefan/7787277/working/3D/511' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1OC(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1C)

`REAL300025497645.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497645.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497645/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497645 none CC1OC(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 6, 7, 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: [8, 8, 8, 8, 8, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 43, 132, 132, 132, 132, 132, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 25, 25, 132, 1, 1, 8, 8, 8, 8] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47, 48, 49, 50])
total number of confs: 267
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497645 none CC1OC(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 6, 7, 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, 201, 201, 201, 201, 201, 201, 132, 132, 132, 132, 132, 101, 47, 101, 13, 1, 1, 1, 1, 1, 1, 1, 132, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 132, 132, 132, 132, 132, 47, 47, 1, 132, 132, 201, 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, 48, 49, 50])
total number of confs: 613
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497645 none CC1OC(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 6, 7, 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: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 27, 27, 69, 107, 201, 201, 201, 201, 201, 8, 1, 1, 2, 2, 2, 1, 1, 2, 2, 2, 1, 3, 8, 8, 8, 8, 8, 69, 69, 201, 8, 8, 1, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 47, 35, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50])
total number of confs: 507
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497645 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497645
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497645/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497645
Building REAL300025497646
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497646'
/scratch/stefan/7787277/working/building/REAL300025497646 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497646

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497646/0 /scratch/stefan/7787277/working/building/REAL300025497646 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 512)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/512
`/scratch/stefan/7787277/working/3D/512' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)(CC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497646.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497646.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497646/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497646 none CCC(C)(CC)C(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [192, 189, 138, 189, 189, 192, 138, 138, 102, 102, 102, 102, 102, 80, 53, 80, 13, 1, 1, 1, 1, 1, 1, 1, 102, 201, 201, 201, 201, 201, 189, 189, 189, 201, 201, 201, 201, 201, 138, 102, 102, 102, 102, 102, 53, 53, 1, 102, 102] 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])
total number of confs: 932
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: REAL300025497646 none CCC(C)(CC)C(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 5, 11, 11, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 27, 102, 102, 102, 102, 102, 1, 14, 14, 14, 14, 14, 11, 11, 11, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 13, 13, 102, 1, 1] 201
rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 259
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497646 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497646
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497646/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497646
Building REAL300025497647
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497647'
/scratch/stefan/7787277/working/building/REAL300025497647 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025497647

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497647/0 /scratch/stefan/7787277/working/building/REAL300025497647 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 513)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/513
`/scratch/stefan/7787277/working/3D/513' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497647.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497647.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497647/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497647 none CCN1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 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]
0  hydrogens 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, 19, 19, 19, 19, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 29, 81, 81, 81, 81, 81, 1, 19, 29, 29, 29, 29, 29, 19, 19, 19, 19, 19, 4, 1, 1, 1, 1, 1, 17, 17, 81, 1, 1, 19, 19] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 48, 49])
total number of confs: 261
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497647 none CCN1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
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, 81, 81, 81, 81, 81, 71, 37, 71, 13, 1, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 122, 81, 81, 81, 81, 81, 37, 37, 1, 81, 81, 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])
total number of confs: 659
number of broken/clashed sets: 61
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497647 none CCN1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 19, 19, 19, 43, 43, 93, 121, 201, 201, 201, 201, 201, 19, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 93, 93, 201, 19, 19, 1, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 48, 49, 35, 36, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 534
number of broken/clashed sets: 61
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497647 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497647/1 /scratch/stefan/7787277/working/building/REAL300025497647 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 514)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/514
`/scratch/stefan/7787277/working/3D/514' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@@H+]1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497647.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497647.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497647/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497647 none CC[N@@H+]1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7]
dock color type numbers: [7, 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]
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, 4, 4, 4, 4, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 19, 46, 46, 46, 46, 46, 1, 4, 6, 6, 6, 6, 6, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 11, 11, 46, 1, 1, 4, 4] 48
rigid atoms, others: [48, 43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49, 50])
total number of confs: 112
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497647 none CC[N@@H+]1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7]
dock color type numbers: [7, 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]
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, 46, 46, 46, 46, 46, 43, 27, 43, 12, 1, 1, 1, 1, 1, 1, 1, 46, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 46, 46, 46, 46, 46, 27, 27, 1, 46, 46, 48, 48] 48
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, 50])
total number of confs: 155
number of broken/clashed sets: 47
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497647 none CC[N@@H+]1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
48  conformations in input
total number of sets (complete confs): 48
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 5, 5, 18, 23, 48, 48, 48, 48, 48, 4, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 18, 18, 48, 4, 4, 1, 1] 48
rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 49, 50, 35, 36, 27, 37] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 122
number of broken/clashed sets: 47
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497647 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `2'
/scratch/stefan/7787277/working/building/REAL300025497647/2 /scratch/stefan/7787277/working/building/REAL300025497647 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 2 (index: 515)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/515
`/scratch/stefan/7787277/working/3D/515' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@H+]1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497647.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025497647.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497647/2/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: REAL300025497647 none CC[N@H+]1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [9, 7, 7, 7, 7, 7, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 8, 18, 18, 18, 18, 18, 1, 7, 9, 9, 9, 9, 9, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 7, 7, 18, 1, 1, 7, 7] 24
rigid atoms, others: [48, 43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49, 50])
total number of confs: 64
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497647 none CC[N@H+]1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 18, 18, 18, 18, 18, 18, 14, 18, 9, 1, 1, 1, 1, 1, 1, 1, 18, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 18, 18, 18, 18, 18, 14, 14, 1, 18, 18, 24, 24] 24
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, 50])
total number of confs: 75
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497647 none CC[N@H+]1CCOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 9, 6, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
24  conformations in input
total number of sets (complete confs): 24
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 10, 10, 15, 16, 24, 24, 24, 24, 24, 7, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 4, 7, 7, 7, 7, 7, 15, 15, 24, 7, 7, 1, 1] 24
rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 49, 50, 35, 36, 27, 37] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 75
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497647 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497647
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497647/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497647/1.*
2: /scratch/stefan/7787277/working/building/REAL300025497647/2.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497647
Building REAL300025497648
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497648'
/scratch/stefan/7787277/working/building/REAL300025497648 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497648

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497648/0 /scratch/stefan/7787277/working/building/REAL300025497648 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 516)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/516
`/scratch/stefan/7787277/working/3D/516' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1)

`REAL300025497648.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497648.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497648/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497648 none CC1CCC(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 18, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 21, 84, 84, 84, 84, 84, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 20, 20, 18, 18, 5, 1, 1, 1, 1, 1, 12, 12, 84, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 49, 50, 41, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48])
total number of confs: 232
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497648 none CC1CCC(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 118, 118, 118, 84, 84, 84, 84, 84, 58, 31, 58, 13, 1, 1, 1, 1, 1, 1, 1, 84, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 118, 84, 84, 84, 84, 84, 31, 31, 1, 84, 84] 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])
total number of confs: 762
number of broken/clashed sets: 78
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497648 none CC1CCC(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 5, 14, 14, 14, 25, 25, 25, 25, 25, 35, 35, 73, 119, 201, 201, 201, 201, 201, 25, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 14, 25, 25, 25, 25, 25, 73, 73, 201, 25, 25] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 35, 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: 521
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497648 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497648
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497648/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497648
Building REAL300025497649
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497649'
/scratch/stefan/7787277/working/building/REAL300025497649 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497649

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497649/0 /scratch/stefan/7787277/working/building/REAL300025497649 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 517)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/517
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C23CCC(CC2)CC3)C1)

`REAL300025497649.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497649.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497649/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497649 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CCC(CC2)CC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [5, 1, 5, 20, 51, 153, 153, 153, 153, 153, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 5, 9, 9, 9, 9, 1, 20, 20, 153, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 5, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 49, 50, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 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])
total number of confs: 294
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497649 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CCC(CC2)CC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [22, 9, 22, 55, 104, 201, 201, 201, 201, 201, 9, 9, 9, 9, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 55, 55, 201, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 201
rigid atoms, others: [16, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 49, 50])
total number of confs: 443
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497649 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CCC(CC2)CC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [116, 50, 13, 1, 1, 1, 1, 1, 1, 1, 116, 153, 153, 153, 153, 153, 198, 198, 198, 201, 201, 198, 201, 201, 201, 201, 153, 50, 50, 1, 153, 153, 153, 153, 153, 198, 201, 201, 201, 201, 198, 201, 201, 201, 201, 201, 201, 201, 201, 153, 153] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 618
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497649 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497649
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497649/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497649
Building REAL300025497650
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497650'
/scratch/stefan/7787277/working/building/REAL300025497650 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497650

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497650/0 /scratch/stefan/7787277/working/building/REAL300025497650 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 518)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/518
`/scratch/stefan/7787277/working/3D/518' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCCC(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497650.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497650.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497650/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497650 none CCCCCC(C)(C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens need 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, 181, 178, 162, 97, 162, 162, 97, 97, 51, 51, 51, 51, 51, 41, 20, 41, 12, 1, 1, 1, 1, 1, 1, 1, 51, 201, 201, 201, 201, 201, 201, 201, 181, 181, 181, 181, 162, 162, 162, 162, 162, 162, 97, 51, 51, 51, 51, 51, 20, 20, 1, 51, 51] 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: 914
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: REAL300025497650 none CCCCCC(C)(C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 28, 21, 19, 11, 4, 11, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 25, 51, 51, 51, 51, 51, 1, 36, 36, 36, 35, 36, 30, 30, 21, 21, 21, 21, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 13, 13, 51, 1, 1] 201
rigid atoms, others: [16, 15, 10, 11, 12, 13, 46, 45, 48, 49, 14, 54, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52])
total number of confs: 286
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497650 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497650
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497650/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497650
Building REAL300025497651
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497651'
/scratch/stefan/7787277/working/building/REAL300025497651 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497651

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497651/0 /scratch/stefan/7787277/working/building/REAL300025497651 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 519)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/519
`/scratch/stefan/7787277/working/3D/519' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCCC(CC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497651.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497651.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497651/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497651 none CCCCCC(CC)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens need 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, 197, 195, 163, 109, 163, 161, 109, 109, 62, 62, 62, 62, 62, 48, 27, 48, 13, 1, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 201, 200, 200, 197, 197, 195, 195, 163, 166, 166, 166, 166, 166, 109, 62, 62, 62, 62, 62, 27, 27, 1, 62, 62] 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: 889
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: REAL300025497651 none CCCCCC(CC)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens 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, 30, 29, 28, 12, 5, 12, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 15, 62, 62, 62, 62, 62, 1, 31, 31, 31, 31, 31, 30, 30, 29, 29, 28, 28, 12, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 8, 8, 62, 1, 1] 201
rigid atoms, others: [16, 15, 10, 11, 12, 13, 46, 45, 48, 49, 14, 54, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52])
total number of confs: 262
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497651 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497651
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497651/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497651
Building REAL300025497652
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497652'
/scratch/stefan/7787277/working/building/REAL300025497652 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497652

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497652/0 /scratch/stefan/7787277/working/building/REAL300025497652 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 520)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/520
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2=CC=C(C3CC3)C=C2)C1)

`REAL300025497652.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497652.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497652/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025497652 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(C3CC3)C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 6, 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: [6, 1, 6, 14, 27, 108, 108, 108, 108, 108, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 5, 5, 18, 18, 9, 9, 1, 14, 14, 108, 1, 1, 1, 1, 1, 5, 9, 9, 18, 18, 18, 18, 18, 9, 9, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 47, 10, 11, 12, 13, 14, 15, 46, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 239
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.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: REAL300025497652 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(C3CC3)C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 6, 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: [37, 18, 37, 57, 99, 201, 201, 201, 201, 201, 18, 18, 18, 18, 8, 8, 4, 8, 3, 5, 5, 1, 1, 1, 1, 5, 5, 18, 57, 57, 201, 18, 18, 18, 18, 18, 8, 5, 5, 1, 1, 1, 1, 1, 5, 5, 18, 18] 201
rigid atoms, others: [39, 40, 41, 42, 43, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 47])
total number of confs: 434
number of broken/clashed sets: 20
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497652 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(C3CC3)C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 6, 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: [20, 9, 20, 31, 53, 135, 135, 135, 135, 135, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 5, 5, 1, 1, 9, 31, 31, 135, 9, 9, 9, 9, 9, 3, 1, 1, 5, 5, 5, 5, 5, 1, 1, 9, 9] 201
rigid atoms, others: [37, 38, 44, 45, 16, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 46, 47])
total number of confs: 273
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497652 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(C3CC3)C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 1, 1, 5, 7, 7, 6, 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: [94, 51, 13, 1, 1, 1, 1, 1, 1, 1, 94, 108, 108, 108, 108, 108, 110, 110, 110, 135, 135, 110, 110, 201, 201, 135, 135, 108, 51, 51, 1, 108, 108, 108, 108, 108, 110, 135, 135, 201, 201, 201, 201, 201, 135, 135, 108, 108] 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: 816
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497652 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497652
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497652/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497652
Building REAL300025497653
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497653'
/scratch/stefan/7787277/working/building/REAL300025497653 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497653

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497653/0 /scratch/stefan/7787277/working/building/REAL300025497653 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 521)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/521
`/scratch/stefan/7787277/working/3D/521' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CCC(C)(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1)

`REAL300025497653.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497653.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497653/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497653 none CC1=CCC(C)(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 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]
0  hydrogens 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, 5, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 40, 103, 103, 103, 103, 103, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 1, 1, 1, 18, 18, 103, 1, 1, 6, 6, 6, 6] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47, 48, 49, 50])
total number of confs: 207
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497653 none CC1=CCC(C)(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 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]
0  hydrogens need rotated
201  conformations 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, 201, 197, 197, 103, 103, 103, 103, 103, 84, 47, 84, 13, 1, 1, 1, 1, 1, 1, 1, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 197, 103, 103, 103, 103, 103, 47, 47, 1, 103, 103, 201, 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, 48, 49, 50])
total number of confs: 603
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497653 none CC1=CCC(C)(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 6, 6, 6, 6, 6, 21, 21, 53, 102, 201, 201, 201, 201, 201, 6, 1, 1, 2, 2, 2, 1, 1, 1, 2, 2, 2, 3, 6, 6, 6, 6, 6, 53, 53, 201, 6, 6, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 47, 48, 49, 50, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 453
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497653 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497653
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497653/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497653
Building REAL300025497654
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497654'
/scratch/stefan/7787277/working/building/REAL300025497654 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497654

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497654/0 /scratch/stefan/7787277/working/building/REAL300025497654 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 522)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/522
`/scratch/stefan/7787277/working/3D/522' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)CC(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497654.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497654.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497654/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497654 none CC(C)(C)CC(C)(C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 129, 129, 129, 90, 32, 89, 13, 1, 1, 1, 1, 1, 1, 1, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 129, 129, 129, 32, 32, 1, 129, 129] 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: 581
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: REAL300025497654 none CC(C)(C)CC(C)(C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 7, 7, 28, 57, 129, 129, 129, 129, 129, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 28, 28, 129, 1, 1] 201
rigid atoms, others: [16, 15, 10, 11, 12, 13, 46, 45, 48, 49, 14, 54, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52])
total number of confs: 260
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497654 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497654
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497654/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497654
Building REAL300025497655
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497655'
/scratch/stefan/7787277/working/building/REAL300025497655 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497655

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497655/0 /scratch/stefan/7787277/working/building/REAL300025497655 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 523)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/523
`/scratch/stefan/7787277/working/3D/523' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CC=C1)

`REAL300025497655.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497655.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497655/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497655 none C=CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 63, 63, 63, 63, 63, 54, 25, 54, 13, 1, 1, 1, 1, 1, 1, 1, 63, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 63, 63, 63, 63, 63, 25, 25, 1, 63, 63, 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])
total number of confs: 736
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497655 none C=CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 16, 16, 33, 33, 33, 33, 33, 45, 45, 70, 113, 201, 201, 201, 201, 201, 33, 1, 1, 1, 1, 1, 1, 7, 7, 7, 4, 16, 33, 33, 33, 33, 33, 70, 70, 201, 33, 33, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 43, 44, 45, 46, 47, 22, 23, 24, 25, 26, 27] set([0, 1, 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])
total number of confs: 475
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497655 none C=CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 7, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 23, 63, 63, 63, 63, 63, 1, 24, 33, 33, 29, 33, 33, 36, 36, 36, 24, 4, 1, 1, 1, 1, 1, 14, 14, 63, 1, 1, 33, 33, 33, 33, 33] 201
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 41, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47])
total number of confs: 275
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497655 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497655
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497655/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497655
Building REAL300025497656
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497656'
/scratch/stefan/7787277/working/building/REAL300025497656 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497656

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497656/0 /scratch/stefan/7787277/working/building/REAL300025497656 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 524)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/524
`/scratch/stefan/7787277/working/3D/524' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCCC1)

`REAL300025497656.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497656.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497656/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497656 none CCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 31, 73, 73, 73, 73, 73, 1, 9, 9, 9, 9, 9, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 17, 17, 73, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 201
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 41, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 198
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497656 none CCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens need rotated
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, 73, 73, 73, 73, 73, 69, 39, 69, 13, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 110, 73, 73, 73, 73, 73, 39, 39, 1, 73, 73, 201, 201, 201, 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, 51, 52])
total number of confs: 726
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497656 none CCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens 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, 3, 3, 3, 9, 9, 9, 9, 9, 30, 30, 81, 121, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 3, 9, 9, 9, 9, 9, 81, 81, 201, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 2, 3, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 22, 23, 24, 25, 26] set([0, 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: 515
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497656 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497656
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497656/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497656
Building REAL300025497657
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497657'
/scratch/stefan/7787277/working/building/REAL300025497657 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497657

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497657/0 /scratch/stefan/7787277/working/building/REAL300025497657 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 525)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/525
`/scratch/stefan/7787277/working/3D/525' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)=N1)

`REAL300025497657.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497657.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497657/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497657 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 6, 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, 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, 25, 25, 25, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 32, 77, 77, 77, 77, 77, 1, 25, 25, 25, 25, 25, 25, 25, 25, 5, 1, 1, 1, 1, 1, 18, 18, 77, 1, 1, 25, 25, 25] 201
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45])
total number of confs: 198
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497657 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 6, 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, 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, 106, 106, 106, 77, 77, 77, 77, 77, 63, 40, 63, 13, 1, 1, 1, 1, 1, 1, 1, 77, 201, 201, 201, 201, 201, 201, 201, 201, 106, 77, 77, 77, 77, 77, 40, 40, 1, 77, 77, 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])
total number of confs: 503
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497657 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 8, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 9, 9, 25, 25, 25, 25, 25, 51, 51, 88, 129, 201, 201, 201, 201, 201, 25, 1, 1, 1, 2, 2, 2, 1, 1, 9, 25, 25, 25, 25, 25, 88, 88, 201, 25, 25, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 553
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497657 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497657
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497657/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497657
Building REAL300025497658
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497658'
/scratch/stefan/7787277/working/building/REAL300025497658 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497658

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497658/0 /scratch/stefan/7787277/working/building/REAL300025497658 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 526)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/526
`/scratch/stefan/7787277/working/3D/526' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCN1N=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497658.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497658.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497658/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497658 none CCCN1N=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens 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, 12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 23, 91, 91, 91, 91, 91, 1, 32, 32, 32, 32, 32, 27, 27, 12, 12, 5, 1, 1, 1, 1, 1, 13, 13, 91, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 271
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497658 none CCCN1N=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 157, 157, 157, 157, 157, 119, 119, 119, 91, 91, 91, 91, 91, 55, 30, 55, 13, 1, 1, 1, 1, 1, 1, 1, 91, 201, 201, 201, 201, 201, 201, 201, 157, 157, 119, 91, 91, 91, 91, 91, 30, 30, 1, 91, 91] 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])
total number of confs: 664
number of broken/clashed sets: 36
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497658 none CCCN1N=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 8, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 24, 24, 47, 66, 157, 157, 157, 157, 157, 12, 9, 9, 9, 9, 9, 6, 6, 1, 1, 4, 12, 12, 12, 12, 12, 47, 47, 157, 12, 12] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 34, 35] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 380
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497658 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497658
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497658/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497658
Building REAL300025497659
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497659'
/scratch/stefan/7787277/working/building/REAL300025497659 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497659

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497659/0 /scratch/stefan/7787277/working/building/REAL300025497659 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 527)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/527
`/scratch/stefan/7787277/working/3D/527' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2C=CC=CC=C2)C1)

`REAL300025497659.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497659.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497659/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497659 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2C=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 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]
0  hydrogens 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, 32, 114, 113, 114, 114, 114, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 1, 17, 17, 114, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 43, 33, 10, 11, 12, 13, 14, 15, 42, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 219
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497659 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2C=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 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]
0  hydrogens 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, 8, 22, 58, 97, 201, 201, 201, 201, 201, 8, 8, 8, 8, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 8, 58, 58, 201, 8, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 1, 8, 8] 201
rigid atoms, others: [35, 36, 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, 42, 43])
total number of confs: 445
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497659 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2C=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [86, 43, 13, 1, 1, 1, 1, 1, 1, 1, 86, 114, 114, 114, 114, 114, 163, 163, 163, 201, 201, 201, 201, 201, 201, 114, 43, 43, 1, 114, 114, 114, 114, 114, 163, 201, 201, 201, 201, 201, 201, 201, 114, 114] 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: 639
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497659 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497659
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497659/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497659
Building REAL300025497660
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497660'
/scratch/stefan/7787277/working/building/REAL300025497660 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497660

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497660/0 /scratch/stefan/7787277/working/building/REAL300025497660 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 528)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/528
`/scratch/stefan/7787277/working/3D/528' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497660.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497660.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497660/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497660 none C=C(C)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 198, 89, 89, 89, 79, 79, 79, 79, 79, 63, 28, 63, 13, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 201, 201, 198, 198, 89, 79, 79, 79, 79, 79, 28, 28, 1, 79, 79] 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])
total number of confs: 790
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: REAL300025497660 none C=C(C)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [39, 22, 39, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 16, 79, 79, 79, 79, 79, 1, 39, 39, 39, 39, 39, 22, 22, 16, 16, 3, 1, 1, 1, 1, 1, 7, 7, 79, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 261
number of broken/clashed sets: 95
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497660 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497660
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497660/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497660
Building REAL300025497661
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497661'
/scratch/stefan/7787277/working/building/REAL300025497661 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497661

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497661/0 /scratch/stefan/7787277/working/building/REAL300025497661 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 529)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/529
`/scratch/stefan/7787277/working/3D/529' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CC=NC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497661.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497661.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497661/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497661 none O=C(CCC1=CC=NC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 8, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 17, 23, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 19, 68, 68, 68, 68, 68, 1, 17, 17, 23, 23, 34, 34, 34, 5, 1, 1, 1, 1, 1, 9, 9, 68, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 44, 10, 11, 12, 13, 14, 15, 16, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 225
number of broken/clashed sets: 62
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497661 none O=C(CCC1=CC=NC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 8, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 182, 199, 201, 201, 201, 201, 201, 68, 68, 68, 68, 68, 47, 27, 47, 13, 1, 1, 1, 1, 1, 1, 1, 68, 182, 182, 199, 199, 201, 201, 201, 105, 68, 68, 68, 68, 68, 27, 27, 1, 68, 68] 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, 43, 44])
total number of confs: 750
number of broken/clashed sets: 62
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497661 none O=C(CCC1=CC=NC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 8, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 10, 6, 1, 1, 1, 1, 1, 1, 1, 25, 25, 34, 34, 34, 34, 34, 45, 45, 78, 122, 201, 201, 201, 201, 201, 34, 10, 10, 6, 6, 1, 1, 1, 25, 34, 34, 34, 34, 34, 78, 78, 201, 34, 34] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 538
number of broken/clashed sets: 62
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497661 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497661
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497661/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497661
Building REAL300025497662
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497662'
/scratch/stefan/7787277/working/building/REAL300025497662 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497662

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497662/0 /scratch/stefan/7787277/working/building/REAL300025497662 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 530)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/530
`/scratch/stefan/7787277/working/3D/530' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025497662.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497662.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497662/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497662 none CN1C=CC(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [30, 30, 30, 30, 23, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 19, 65, 65, 65, 65, 65, 1, 30, 30, 30, 30, 30, 30, 23, 23, 20, 20, 5, 1, 1, 1, 1, 1, 11, 11, 65, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 210
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497662 none CN1C=CC(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 200, 190, 112, 112, 112, 65, 65, 65, 65, 65, 51, 28, 51, 13, 1, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 201, 200, 200, 190, 190, 112, 65, 65, 65, 65, 65, 28, 28, 1, 65, 65] 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])
total number of confs: 774
number of broken/clashed sets: 60
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497662 none CN1C=CC(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 10, 17, 17, 17, 30, 30, 30, 30, 30, 40, 40, 79, 120, 201, 201, 201, 201, 201, 30, 1, 2, 2, 2, 1, 1, 6, 6, 10, 10, 17, 30, 30, 30, 30, 30, 79, 79, 201, 30, 30] 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: 552
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497662 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497662
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497662/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497662
Building REAL300025497663
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497663'
/scratch/stefan/7787277/working/building/REAL300025497663 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497663

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497663/0 /scratch/stefan/7787277/working/building/REAL300025497663 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 531)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/531
`/scratch/stefan/7787277/working/3D/531' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC=C1CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497663.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497663.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497663/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497663 none CN1N=CC=C1CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens 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, 26, 24, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 13, 54, 54, 54, 54, 54, 1, 38, 38, 38, 38, 38, 26, 26, 24, 24, 5, 1, 1, 1, 1, 1, 6, 6, 54, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 193
number of broken/clashed sets: 62
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497663 none CN1N=CC=C1CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 158, 156, 77, 77, 77, 54, 54, 54, 54, 54, 43, 26, 43, 13, 1, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 201, 158, 158, 156, 156, 77, 54, 54, 54, 54, 54, 26, 26, 1, 54, 54] 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])
total number of confs: 693
number of broken/clashed sets: 62
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497663 none CN1N=CC=C1CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total 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, 5, 21, 21, 21, 38, 38, 38, 38, 38, 52, 52, 93, 139, 201, 201, 201, 201, 201, 38, 2, 2, 2, 1, 1, 3, 3, 5, 5, 21, 38, 38, 38, 38, 38, 93, 93, 201, 38, 38] 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: 579
number of broken/clashed sets: 62
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497663 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497663
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497663/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497663
Building REAL300025497664
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497664'
/scratch/stefan/7787277/working/building/REAL300025497664 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497664

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497664/0 /scratch/stefan/7787277/working/building/REAL300025497664 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 532)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/532
`/scratch/stefan/7787277/working/3D/532' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=C(C=CO3)N2)C1)

`REAL300025497664.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497664.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497664/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497664 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=C(C=CO3)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 32, 56, 149, 149, 149, 149, 149, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 1, 32, 32, 149, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 41, 10, 11, 12, 13, 14, 15, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39])
total number of confs: 308
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497664 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=C(C=CO3)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [41, 14, 41, 96, 128, 201, 201, 201, 201, 201, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 14, 96, 96, 201, 14, 14, 14, 14, 14, 4, 1, 1, 1, 1, 14, 14] 201
rigid atoms, others: [36, 37, 38, 39, 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, 40, 41])
total number of confs: 533
number of broken/clashed sets: 24
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497664 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=C(C=CO3)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'N.pl3', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 12, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7]
dock 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [108, 44, 13, 1, 1, 1, 1, 1, 1, 1, 108, 149, 149, 149, 149, 149, 191, 191, 191, 201, 201, 201, 201, 201, 201, 201, 148, 44, 44, 1, 149, 149, 149, 149, 149, 191, 201, 201, 201, 201, 149, 149] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 590
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497664 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497664
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497664/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497664
Building REAL300025497665
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497665'
/scratch/stefan/7787277/working/building/REAL300025497665 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497665

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497665/0 /scratch/stefan/7787277/working/building/REAL300025497665 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 533)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/533
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2=CC=NS2)C1)

`REAL300025497665.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497665.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497665/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497665 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 14, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 34, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 1, 16, 16, 100, 1, 1, 1, 1, 1, 5, 11, 11, 1, 1] 201
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34])
total number of confs: 199
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497665 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 14, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 11, 32, 66, 100, 201, 201, 201, 201, 201, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 11, 66, 66, 201, 11, 11, 11, 11, 11, 4, 1, 1, 11, 11] 201
rigid atoms, others: [33, 34, 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, 35, 36])
total number of confs: 458
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497665 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 14, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 39, 13, 1, 1, 1, 1, 1, 1, 1, 77, 100, 100, 100, 100, 100, 154, 154, 154, 201, 201, 201, 201, 100, 39, 39, 1, 100, 100, 100, 100, 100, 154, 201, 201, 100, 100] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 598
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497665 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497665
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497665/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497665
Building REAL300025497666
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497666'
/scratch/stefan/7787277/working/building/REAL300025497666 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497666

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497666/0 /scratch/stefan/7787277/working/building/REAL300025497666 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 534)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/534
`/scratch/stefan/7787277/working/3D/534' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)C(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)OCC)

`REAL300025497666.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497666.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497666/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497666 none C=C(C)C(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)OCC 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.2', 'C.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 6, 4, 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, 7]
0  hydrogens need rotated
201  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, 164, 164, 164, 118, 118, 118, 118, 118, 89, 33, 89, 13, 1, 1, 1, 1, 1, 1, 1, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 164, 118, 118, 118, 118, 118, 33, 33, 1, 118, 118, 201, 201, 201, 201, 201] 201
rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 673
number of broken/clashed sets: 91
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497666 none C=C(C)C(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)OCC 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.2', 'C.2', 'C.3', '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', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 6, 4, 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, 7]
0  hydrogens 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, 18, 23, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 13, 27, 118, 118, 118, 118, 118, 1, 18, 21, 21, 23, 23, 23, 23, 23, 18, 12, 12, 5, 1, 1, 1, 1, 1, 13, 13, 118, 1, 1, 21, 21, 21, 21, 21] 201
rigid atoms, others: [45, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49, 50])
total number of confs: 278
number of broken/clashed sets: 91
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497666 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497666
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497666/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497666
Building REAL300025497667
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497667'
/scratch/stefan/7787277/working/building/REAL300025497667 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497667

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497667/0 /scratch/stefan/7787277/working/building/REAL300025497667 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 535)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/535
`/scratch/stefan/7787277/working/3D/535' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1)

`REAL300025497667.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497667.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497667/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497667 none CCC1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens 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, 22, 22, 22, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 35, 100, 100, 100, 100, 100, 1, 22, 34, 34, 34, 34, 34, 22, 22, 22, 22, 22, 22, 4, 1, 1, 1, 1, 1, 21, 21, 100, 1, 1] 201
rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 40, 46, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 314
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497667 none CCC1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 145, 145, 145, 100, 100, 100, 100, 100, 82, 38, 82, 13, 1, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 145, 100, 100, 100, 100, 100, 38, 38, 1, 100, 100] 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: 655
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497667 none CCC1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need 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, 10, 10, 10, 22, 22, 22, 22, 22, 48, 48, 93, 120, 201, 201, 201, 201, 201, 22, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 22, 22, 22, 22, 22, 93, 93, 201, 22, 22] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 35, 25, 36, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 536
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497667 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497667
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497667/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497667
Building REAL300025497668
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497668'
/scratch/stefan/7787277/working/building/REAL300025497668 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497668

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497668/0 /scratch/stefan/7787277/working/building/REAL300025497668 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 536)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/536
`/scratch/stefan/7787277/working/3D/536' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(Cl)=NN1)

`REAL300025497668.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497668.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497668/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497668 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(Cl)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 16, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 35, 111, 111, 111, 111, 111, 1, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 17, 17, 111, 1, 1, 13] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 21, 39, 38, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40])
total number of confs: 216
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497668 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(Cl)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 16, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 132, 132, 132, 111, 111, 111, 111, 111, 85, 45, 85, 13, 1, 1, 1, 1, 1, 1, 1, 111, 201, 201, 201, 201, 201, 201, 201, 132, 111, 111, 111, 111, 111, 45, 45, 1, 111, 111, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 518
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497668 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(Cl)=NN1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 16, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 38, 38, 69, 104, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 2, 2, 2, 6, 13, 13, 13, 13, 13, 69, 69, 201, 13, 13, 1] 201
rigid atoms, others: [0, 1, 2, 3, 40, 22, 23, 24, 25] set([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])
total number of confs: 503
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497668 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497668
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497668/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497668
Building REAL300025497669
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497669'
/scratch/stefan/7787277/working/building/REAL300025497669 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497669

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497669/0 /scratch/stefan/7787277/working/building/REAL300025497669 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 537)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/537
`/scratch/stefan/7787277/working/3D/537' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1)

`REAL300025497669.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497669.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497669/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497669 none COCCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 20, 16, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 25, 86, 86, 86, 86, 86, 1, 13, 13, 25, 25, 25, 20, 20, 16, 16, 5, 1, 1, 1, 1, 1, 14, 14, 86, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47])
total number of confs: 224
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497669 none COCCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
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, 188, 116, 116, 116, 86, 86, 86, 86, 86, 61, 29, 61, 13, 1, 1, 1, 1, 1, 1, 1, 86, 188, 188, 201, 201, 201, 201, 201, 190, 190, 116, 86, 86, 86, 86, 86, 29, 29, 1, 86, 86, 188, 188, 188, 188] 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: 656
number of broken/clashed sets: 82
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497669 none COCCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 6, 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]
0  hydrogens 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, 4, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 22, 22, 57, 98, 188, 188, 188, 188, 188, 13, 1, 1, 13, 13, 13, 7, 7, 4, 4, 5, 13, 13, 13, 13, 13, 57, 57, 188, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [3, 4, 5, 44, 45, 46, 47, 24, 25] set([0, 1, 2, 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: 472
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497669 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497669
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497669/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497669
Building REAL300025497670
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497670'
/scratch/stefan/7787277/working/building/REAL300025497670 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497670

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497670/0 /scratch/stefan/7787277/working/building/REAL300025497670 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 538)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/538
`/scratch/stefan/7787277/working/3D/538' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1)

`REAL300025497670.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497670.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497670/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497670 none CC(C)CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 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, 7, 7]
0  hydrogens 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, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 31, 73, 73, 73, 73, 73, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 16, 16, 73, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [45, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49])
total number of confs: 177
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497670 none CC(C)CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 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, 7, 7]
0  hydrogens need rotated
201  conformations 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, 73, 73, 73, 73, 73, 56, 23, 56, 13, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 121, 73, 73, 73, 73, 73, 23, 23, 1, 73, 73, 201, 201, 201, 201] 201
rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49])
total number of confs: 646
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497670 none CC(C)CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 32, 32, 69, 115, 201, 201, 201, 201, 201, 13, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 13, 13, 13, 13, 13, 69, 69, 201, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [3, 4, 5, 46, 47, 48, 49, 24, 25] set([0, 1, 2, 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: 479
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497670 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497670
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497670/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497670
Building REAL300025497671
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497671'
/scratch/stefan/7787277/working/building/REAL300025497671 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497671

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497671/0 /scratch/stefan/7787277/working/building/REAL300025497671 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 539)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/539
`/scratch/stefan/7787277/working/3D/539' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C)

`REAL300025497671.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497671.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497671/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497671 none CC1=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 25, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 12, 50, 50, 50, 50, 50, 1, 44, 44, 44, 44, 44, 44, 44, 25, 25, 5, 1, 1, 1, 1, 1, 7, 7, 50, 1, 1, 44, 44, 44, 44] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46])
total number of confs: 194
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497671 none CC1=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 67, 67, 67, 50, 50, 50, 50, 50, 40, 27, 40, 12, 1, 1, 1, 1, 1, 1, 1, 50, 201, 201, 201, 201, 201, 201, 201, 166, 166, 67, 50, 50, 50, 50, 50, 27, 27, 1, 50, 50, 201, 201, 201, 201] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46])
total number of confs: 699
number of broken/clashed sets: 47
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497671 none CC1=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 25, 25, 25, 44, 44, 44, 44, 44, 55, 55, 91, 128, 201, 201, 201, 201, 201, 44, 1, 1, 1, 1, 2, 2, 2, 6, 6, 25, 44, 44, 44, 44, 44, 91, 91, 201, 44, 44, 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: 563
number of broken/clashed sets: 47
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497671 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497671
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497671/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497671
Building REAL300025497672
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497672'
/scratch/stefan/7787277/working/building/REAL300025497672 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497672

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497672/0 /scratch/stefan/7787277/working/building/REAL300025497672 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 540)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/540
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2=C(C3CC3)C=CN2)C1)

`REAL300025497672.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497672.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497672/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025497672 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(C3CC3)C=CN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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, 12, 21, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 1, 4, 4, 4, 18, 18, 26, 26, 18, 18, 18, 1, 12, 12, 79, 1, 1, 1, 1, 1, 4, 26, 26, 26, 26, 26, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 44, 10, 11, 12, 13, 14, 15, 45, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 186
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.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: REAL300025497672 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(C3CC3)C=CN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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: [54, 26, 54, 82, 120, 201, 201, 201, 201, 201, 26, 26, 26, 26, 17, 17, 7, 17, 7, 1, 1, 1, 1, 7, 7, 6, 26, 82, 82, 201, 26, 26, 26, 26, 26, 17, 1, 1, 1, 1, 1, 7, 7, 7, 26, 26] 201
rigid atoms, others: [36, 37, 38, 39, 40, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45])
total number of confs: 506
number of broken/clashed sets: 35
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497672 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(C3CC3)C=CN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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: [41, 18, 41, 66, 103, 179, 179, 179, 179, 179, 18, 18, 18, 18, 9, 9, 1, 9, 1, 1, 1, 7, 7, 1, 1, 1, 18, 66, 66, 179, 18, 18, 18, 18, 18, 9, 7, 7, 7, 7, 7, 1, 1, 1, 18, 18] 201
rigid atoms, others: [41, 42, 43, 16, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45])
total number of confs: 450
number of broken/clashed sets: 35
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497672 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(C3CC3)C=CN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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: [61, 33, 12, 1, 1, 1, 1, 1, 1, 1, 61, 79, 79, 79, 79, 79, 127, 127, 127, 179, 179, 201, 201, 179, 179, 179, 79, 33, 33, 1, 79, 79, 79, 79, 79, 127, 201, 201, 201, 201, 201, 179, 179, 179, 79, 79] 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: 577
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497672 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497672
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497672/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497672
Building REAL300025497673
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497673'
/scratch/stefan/7787277/working/building/REAL300025497673 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497673

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497673/0 /scratch/stefan/7787277/working/building/REAL300025497673 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 541)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/541
`/scratch/stefan/7787277/working/3D/541' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(C)C(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497673.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497673.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497673/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497673 none COCC(C)C(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 168, 168, 168, 112, 168, 112, 112, 73, 73, 73, 73, 73, 65, 33, 64, 13, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 168, 168, 168, 168, 168, 168, 168, 168, 112, 73, 73, 73, 73, 73, 33, 33, 1, 73, 73] 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: 862
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497673 none COCC(C)C(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 12, 10, 12, 4, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 20, 73, 73, 73, 73, 73, 1, 40, 40, 40, 28, 28, 12, 12, 12, 12, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 10, 10, 73, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 263
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497673 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497673
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497673/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497673
Building REAL300025497674
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497674'
/scratch/stefan/7787277/working/building/REAL300025497674 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497674

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497674/0 /scratch/stefan/7787277/working/building/REAL300025497674 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 542)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/542
`/scratch/stefan/7787277/working/3D/542' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC(F)F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497674.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497674.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497674/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497674 none CCC(CC(F)F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 1, 1, 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, 6, 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: [163, 184, 73, 184, 201, 201, 201, 73, 73, 39, 39, 39, 39, 39, 39, 38, 39, 13, 1, 1, 1, 1, 1, 1, 1, 39, 186, 186, 186, 186, 186, 184, 201, 201, 201, 73, 39, 39, 39, 39, 39, 38, 38, 1, 39, 39] 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])
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: REAL300025497674 none CCC(CC(F)F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 1, 1, 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, 6, 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: [22, 21, 5, 21, 33, 39, 39, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 39, 39, 39, 39, 39, 1, 27, 27, 27, 27, 27, 21, 33, 33, 39, 5, 1, 1, 1, 1, 1, 6, 6, 39, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 303
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497674 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497674
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497674/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497674
Building REAL300025497675
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497675'
/scratch/stefan/7787277/working/building/REAL300025497675 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497675

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497675/0 /scratch/stefan/7787277/working/building/REAL300025497675 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 543)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/543
`/scratch/stefan/7787277/working/3D/543' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(CC(F)F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497675.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497675.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497675/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497675 none CC(C)(CC(F)F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 1, 1, 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, 6, 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
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [22, 13, 22, 22, 27, 27, 27, 13, 13, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1, 1, 1, 1, 1, 1, 1, 9, 22, 22, 22, 22, 22, 22, 27, 27, 27, 13, 9, 9, 9, 9, 9, 9, 9, 1, 9, 9] 27
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])
total number of confs: 111
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: REAL300025497675 none CC(C)(CC(F)F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 1, 1, 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, 6, 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
27  conformations in input
total number of sets (complete confs): 27
using default count positions algorithm for smaller data
unique positions, atoms: [13, 6, 13, 13, 17, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 9, 9, 9, 9, 9, 1, 13, 13, 13, 13, 13, 13, 17, 17, 19, 6, 1, 1, 1, 1, 1, 7, 7, 9, 1, 1] 27
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 108
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497675 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497675
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497675/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497675
Building REAL300025497676
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497676'
/scratch/stefan/7787277/working/building/REAL300025497676 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497676

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497676/0 /scratch/stefan/7787277/working/building/REAL300025497676 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 544)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/544
`/scratch/stefan/7787277/working/3D/544' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCC(=O)NC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497676.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497676.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497676/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497676 none O=C(CC1CCC(=O)NC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 11, 8, 5, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 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, 5, 5, 25, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 24, 80, 80, 80, 80, 80, 1, 25, 25, 39, 39, 39, 39, 39, 39, 39, 39, 5, 1, 1, 1, 1, 1, 14, 14, 80, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 274
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497676 none O=C(CC1CCC(=O)NC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 11, 8, 5, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 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: [109, 109, 109, 194, 201, 201, 201, 201, 201, 201, 80, 80, 80, 80, 80, 50, 30, 50, 13, 1, 1, 1, 1, 1, 1, 1, 80, 194, 194, 201, 201, 201, 201, 201, 201, 201, 201, 109, 80, 80, 80, 80, 80, 30, 30, 1, 80, 80] 201
rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47])
total number of confs: 729
number of broken/clashed sets: 42
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497676 none O=C(CC1CCC(=O)NC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 11, 8, 5, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 6, 4, 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: [23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 39, 39, 39, 39, 39, 52, 52, 86, 125, 201, 201, 201, 201, 201, 39, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 23, 39, 39, 39, 39, 39, 86, 86, 201, 39, 39] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 534
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497676 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497676
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497676/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497676
Building REAL300025497677
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497677'
/scratch/stefan/7787277/working/building/REAL300025497677 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497677

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497677/0 /scratch/stefan/7787277/working/building/REAL300025497677 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 545)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/545
`/scratch/stefan/7787277/working/3D/545' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CC2CCC1O2)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497677.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497677.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497677/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497677 none O=C(CC1CC2CCC1O2)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens 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, 24, 43, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 15, 68, 68, 68, 68, 68, 1, 24, 24, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 1, 1, 1, 1, 1, 8, 8, 68, 1, 1] 201
rigid atoms, others: [48, 43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 252
number of broken/clashed sets: 65
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497677 none O=C(CC1CC2CCC1O2)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 104, 189, 201, 201, 201, 201, 201, 201, 68, 68, 68, 68, 68, 52, 29, 52, 13, 1, 1, 1, 1, 1, 1, 1, 68, 189, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 104, 68, 68, 68, 68, 68, 29, 29, 1, 68, 68] 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])
total number of confs: 778
number of broken/clashed sets: 65
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497677 none O=C(CC1CC2CCC1O2)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens 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, 1, 1, 23, 23, 43, 43, 43, 43, 43, 60, 60, 99, 140, 201, 201, 201, 201, 201, 43, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 43, 43, 43, 43, 43, 99, 99, 201, 43, 43] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 37, 35, 36, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 575
number of broken/clashed sets: 65
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497677 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497677
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497677/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497677
Building REAL300025497678
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497678'
/scratch/stefan/7787277/working/building/REAL300025497678 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497678

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497678/0 /scratch/stefan/7787277/working/building/REAL300025497678 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 546)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/546
`/scratch/stefan/7787277/working/3D/546' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1N=NC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497678.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497678.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497678/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497678 none CCN1N=NC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 12, 12, 12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 82, 82, 82, 82, 82, 1, 21, 21, 21, 21, 21, 12, 12, 12, 5, 1, 1, 1, 1, 1, 13, 13, 82, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 44, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 221
number of broken/clashed sets: 56
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497678 none CCN1N=NC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need 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, 156, 156, 156, 114, 114, 114, 82, 82, 82, 82, 82, 46, 28, 46, 13, 1, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 201, 201, 156, 156, 156, 114, 82, 82, 82, 82, 82, 28, 28, 1, 82, 82] 201
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, 44, 45])
total number of confs: 678
number of broken/clashed sets: 56
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497678 none CCN1N=NC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 8, 8, 8, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 22, 22, 38, 58, 156, 156, 156, 156, 156, 12, 3, 3, 3, 3, 3, 2, 2, 2, 6, 12, 12, 12, 12, 12, 38, 38, 156, 12, 12] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 335
number of broken/clashed sets: 56
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497678 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497678
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497678/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497678
Building REAL300025497679
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497679'
/scratch/stefan/7787277/working/building/REAL300025497679 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497679

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497679/0 /scratch/stefan/7787277/working/building/REAL300025497679 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 547)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/547
`/scratch/stefan/7787277/working/3D/547' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=NOC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497679.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497679.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497679/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497679 none CC(C)C1=NOC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 33, 133, 133, 133, 133, 133, 1, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 16, 16, 133, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 44, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 239
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497679 none CC(C)C1=NOC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
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, 179, 179, 179, 133, 133, 133, 133, 133, 78, 31, 78, 13, 1, 1, 1, 1, 1, 1, 1, 133, 201, 201, 201, 201, 201, 201, 201, 201, 179, 133, 133, 133, 133, 133, 31, 31, 1, 133, 133] 201
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, 44, 45])
total number of confs: 538
number of broken/clashed sets: 54
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497679 none CC(C)C1=NOC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 17, 17, 17, 46, 46, 87, 125, 201, 201, 201, 201, 201, 17, 2, 2, 2, 1, 2, 2, 2, 1, 8, 17, 17, 17, 17, 17, 87, 87, 201, 17, 17] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 30] set([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])
total number of confs: 529
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497679 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497679
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497679/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497679
Building REAL300025497680
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497680'
/scratch/stefan/7787277/working/building/REAL300025497680 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497680

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497680/0 /scratch/stefan/7787277/working/building/REAL300025497680 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 548)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/548
`/scratch/stefan/7787277/working/3D/548' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCNC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497680.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497680.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497680/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497680 none O=C(CC1CCNC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 17, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 27, 91, 91, 91, 91, 91, 1, 17, 17, 29, 29, 29, 29, 29, 29, 5, 1, 1, 1, 1, 1, 16, 16, 91, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 261
number of broken/clashed sets: 56
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497680 none O=C(CC1CCNC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 195, 201, 201, 201, 201, 201, 91, 91, 91, 91, 91, 58, 30, 58, 13, 1, 1, 1, 1, 1, 1, 1, 91, 195, 195, 201, 201, 201, 201, 201, 201, 135, 91, 91, 91, 91, 91, 30, 30, 1, 91, 91] 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])
total number of confs: 728
number of broken/clashed sets: 56
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497680 none O=C(CC1CCNC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 8, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15, 29, 29, 29, 29, 29, 47, 47, 86, 126, 201, 201, 201, 201, 201, 29, 7, 7, 1, 1, 1, 1, 1, 1, 15, 29, 29, 29, 29, 29, 86, 86, 201, 29, 29] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 543
number of broken/clashed sets: 56
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497680 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497680
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497680/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497680
Building REAL300025497681
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497681'
/scratch/stefan/7787277/working/building/REAL300025497681 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497681

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497681/0 /scratch/stefan/7787277/working/building/REAL300025497681 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 549)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/549
`/scratch/stefan/7787277/working/3D/549' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@]23C[C@H]2COC3)C1)

`REAL300025497681.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497681.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497681/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497681 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@]23C[C@H]2COC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [6, 1, 6, 15, 30, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 14, 1, 15, 15, 92, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 14, 14, 1, 1] 201
rigid atoms, others: [32, 1, 33, 41, 10, 11, 12, 13, 14, 15, 42, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 186
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497681 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@]23C[C@H]2COC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [34, 14, 34, 67, 104, 201, 201, 201, 201, 201, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 14, 67, 67, 201, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 1, 14, 14] 201
rigid atoms, others: [35, 36, 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, 41, 42])
total number of confs: 473
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497681 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@]23C[C@H]2COC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 7, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [62, 44, 13, 1, 1, 1, 1, 1, 1, 1, 62, 92, 92, 92, 92, 92, 120, 120, 120, 201, 201, 201, 201, 201, 201, 92, 44, 44, 1, 92, 92, 92, 92, 92, 120, 201, 201, 201, 201, 201, 201, 92, 92] 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: 507
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497681 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497681
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497681/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497681
Building REAL300025497682
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497682'
/scratch/stefan/7787277/working/building/REAL300025497682 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
Protomer extracton resulted in 0 protomers
Marking REAL300025497682 as failed and skipping
/scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `/scratch/stefan/7787277/failed'
`/scratch/stefan/7787277/working/building/REAL300025497682' -> `/scratch/stefan/7787277/failed/REAL300025497682'
Building REAL300025497683
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497683'
/scratch/stefan/7787277/working/building/REAL300025497683 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497683

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497683/0 /scratch/stefan/7787277/working/building/REAL300025497683 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 550)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/550
`/scratch/stefan/7787277/working/3D/550' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(F)C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497683.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497683.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497683/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497683 none CC1=C(F)C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens 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, 23, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 29, 72, 72, 72, 72, 72, 1, 23, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 1, 16, 16, 72, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 183
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497683 none CC1=C(F)C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
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, 93, 93, 93, 72, 72, 72, 72, 72, 61, 36, 61, 13, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 201, 201, 93, 72, 72, 72, 72, 72, 36, 36, 1, 72, 72] 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, 42, 43])
total number of confs: 476
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497683 none CC1=C(F)C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 15, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 23, 23, 23, 54, 54, 91, 133, 201, 201, 201, 201, 201, 23, 2, 2, 2, 1, 1, 1, 9, 23, 23, 23, 23, 23, 91, 91, 201, 23, 23] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 546
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497683 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497683
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497683/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497683
Building REAL300025497684
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497684'
/scratch/stefan/7787277/working/building/REAL300025497684 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497684

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497684/0 /scratch/stefan/7787277/working/building/REAL300025497684 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 551)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/551
`/scratch/stefan/7787277/working/3D/551' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1)

`REAL300025497684.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497684.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497684/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497684 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 24, 90, 90, 90, 90, 90, 1, 16, 16, 16, 16, 16, 4, 1, 1, 1, 1, 1, 12, 12, 90, 1, 1, 16, 16, 16, 16] 201
rigid atoms, others: [35, 4, 5, 6, 7, 8, 9, 10, 20, 36, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 32, 33, 34, 37, 38, 39, 40])
total number of confs: 183
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497684 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 6, 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]
0  hydrogens need 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, 90, 90, 90, 90, 90, 80, 50, 80, 13, 1, 1, 1, 1, 1, 1, 1, 90, 201, 201, 201, 201, 201, 120, 90, 90, 90, 90, 90, 50, 50, 1, 90, 90, 201, 201, 201, 201] 201
rigid atoms, others: [34, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40])
total number of confs: 725
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497684 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  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, 16, 16, 16, 16, 16, 35, 35, 60, 99, 201, 201, 201, 201, 201, 16, 1, 1, 2, 2, 2, 6, 16, 16, 16, 16, 16, 60, 60, 201, 16, 16, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 37, 38, 39, 40, 21, 22] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 459
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497684 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497684
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497684/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497684
Building REAL300025497685
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497685'
/scratch/stefan/7787277/working/building/REAL300025497685 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497685

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497685/0 /scratch/stefan/7787277/working/building/REAL300025497685 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 552)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/552
`/scratch/stefan/7787277/working/3D/552' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1F)

`REAL300025497685.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497685.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497685/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497685 none CC1=CC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 44, 131, 131, 131, 131, 131, 1, 18, 18, 18, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 25, 25, 131, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 275
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497685 none CC1=CC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 131, 131, 131, 131, 131, 100, 42, 100, 13, 1, 1, 1, 1, 1, 1, 1, 131, 201, 201, 201, 201, 201, 201, 201, 201, 184, 131, 131, 131, 131, 131, 42, 42, 1, 131, 131] 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])
total number of confs: 601
number of broken/clashed sets: 24
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497685 none CC1=CC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 15, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 18, 18, 18, 18, 18, 47, 47, 92, 125, 201, 201, 201, 201, 201, 18, 1, 1, 2, 2, 2, 1, 1, 1, 8, 18, 18, 18, 18, 18, 92, 92, 201, 18, 18] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 547
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497685 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497685
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497685/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497685
Building REAL300025497686
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497686'
/scratch/stefan/7787277/working/building/REAL300025497686 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497686

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497686/0 /scratch/stefan/7787277/working/building/REAL300025497686 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 553)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/553
`/scratch/stefan/7787277/working/3D/553' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(Cl)C=CS2)C1)

`REAL300025497686.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497686.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497686/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497686 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(Cl)C=CS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 16, 1, 1, 14, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 19, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 12, 12, 52, 1, 1, 1, 1, 1, 5, 15, 15, 1, 1] 201
rigid atoms, others: [32, 1, 36, 37, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35])
total number of confs: 128
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497686 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(Cl)C=CS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 16, 1, 1, 14, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 15, 36, 74, 103, 201, 201, 201, 201, 201, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 15, 74, 74, 201, 15, 15, 15, 15, 15, 5, 1, 1, 15, 15] 201
rigid atoms, others: [34, 35, 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, 36, 37])
total number of confs: 491
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497686 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C(Cl)C=CS2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'S.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 16, 1, 1, 14, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 13, 1, 1, 1, 1, 1, 1, 1, 39, 52, 52, 52, 52, 52, 69, 69, 69, 201, 201, 201, 201, 201, 52, 32, 32, 1, 52, 52, 52, 52, 52, 69, 201, 201, 52, 52] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 414
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497686 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497686
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497686/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497686
Building REAL300025497687
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497687'
/scratch/stefan/7787277/working/building/REAL300025497687 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497687

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497687/0 /scratch/stefan/7787277/working/building/REAL300025497687 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 554)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/554
`/scratch/stefan/7787277/working/3D/554' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCCC1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497687.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497687.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497687/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497687 none CC1CCCC1CC(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 24, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 57, 57, 57, 57, 57, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 24, 24, 5, 1, 1, 1, 1, 1, 6, 6, 57, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 193
number of broken/clashed sets: 64
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497687 none CC1CCCC1CC(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 90, 90, 90, 57, 57, 57, 57, 57, 45, 27, 45, 13, 1, 1, 1, 1, 1, 1, 1, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 90, 57, 57, 57, 57, 57, 27, 27, 1, 57, 57] 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: 779
number of broken/clashed sets: 64
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497687 none CC1CCCC1CC(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 17, 17, 17, 31, 31, 31, 31, 31, 46, 46, 80, 125, 201, 201, 201, 201, 201, 31, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 31, 31, 31, 31, 31, 80, 80, 201, 31, 31] 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])
total number of confs: 543
number of broken/clashed sets: 64
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497687 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497687
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497687/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497687
Building REAL300025497688
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497688'
/scratch/stefan/7787277/working/building/REAL300025497688 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497688

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497688/0 /scratch/stefan/7787277/working/building/REAL300025497688 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 555)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/555
`/scratch/stefan/7787277/working/3D/555' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(=O)NC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497688.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497688.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497688/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497688 none CCC(=O)NC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 138, 72, 138, 72, 72, 65, 65, 65, 65, 65, 51, 27, 50, 13, 1, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 140, 138, 138, 138, 138, 72, 65, 65, 65, 65, 65, 27, 27, 1, 65, 65] 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])
total number of confs: 883
number of broken/clashed sets: 72
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497688 none CCC(=O)NC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 9, 9, 8, 4, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 17, 65, 65, 65, 65, 65, 1, 33, 33, 33, 33, 33, 9, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 9, 9, 65, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 222
number of broken/clashed sets: 72
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497688 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497688
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497688/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497688
Building REAL300025497689
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497689'
/scratch/stefan/7787277/working/building/REAL300025497689 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497689

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497689/0 /scratch/stefan/7787277/working/building/REAL300025497689 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 556)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/556
`/scratch/stefan/7787277/working/3D/556' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(=O)N(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497689.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497689.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497689/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497689 none CC(C)C(=O)N(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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, 201, 201, 201, 201, 193, 201, 95, 95, 95, 59, 59, 59, 59, 59, 42, 28, 42, 13, 1, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 193, 95, 59, 59, 59, 59, 59, 28, 28, 1, 59, 59] 201
rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49])
total number of confs: 746
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: REAL300025497689 none CC(C)C(=O)N(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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: [40, 25, 40, 23, 25, 19, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 59, 59, 59, 59, 59, 1, 40, 40, 40, 40, 40, 40, 40, 23, 23, 23, 19, 19, 5, 1, 1, 1, 1, 1, 8, 8, 59, 1, 1] 201
rigid atoms, others: [48, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 272
number of broken/clashed sets: 71
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497689 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497689
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497689/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497689
Building REAL300025497690
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497690'
/scratch/stefan/7787277/working/building/REAL300025497690 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497690

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497690/0 /scratch/stefan/7787277/working/building/REAL300025497690 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 557)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/557
`/scratch/stefan/7787277/working/3D/557' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC1)

`REAL300025497690.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497690.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497690/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497690 none CN(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 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, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 119, 59, 59, 59, 45, 45, 45, 45, 45, 36, 25, 36, 13, 1, 1, 1, 1, 1, 1, 1, 45, 132, 132, 132, 201, 201, 132, 132, 132, 119, 119, 59, 45, 45, 45, 45, 45, 25, 25, 1, 45, 45, 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])
total number of confs: 805
number of broken/clashed sets: 64
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497690 none CN(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 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, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 4, 6, 11, 24, 24, 24, 35, 35, 35, 35, 35, 44, 44, 73, 116, 201, 201, 201, 201, 201, 35, 1, 4, 1, 1, 1, 6, 6, 6, 11, 11, 24, 35, 35, 35, 35, 35, 73, 73, 201, 35, 35, 1, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 47, 22, 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, 23, 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: 64
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497690 none CN(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(=O)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 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, 7, 6, 4, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 45, 45, 45, 45, 45, 1, 18, 20, 20, 35, 35, 18, 18, 18, 16, 16, 4, 1, 1, 1, 1, 1, 5, 5, 45, 1, 1, 35, 35, 35, 35, 35] 201
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 41, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47])
total number of confs: 199
number of broken/clashed sets: 64
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497690 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497690
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497690/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497690
Building REAL300025497691
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497691'
/scratch/stefan/7787277/working/building/REAL300025497691 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497691

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497691/0 /scratch/stefan/7787277/working/building/REAL300025497691 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 558)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/558
`/scratch/stefan/7787277/working/3D/558' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)N(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497691.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497691.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497691/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497691 none COCC(=O)N(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 165, 164, 165, 163, 164, 59, 59, 59, 59, 59, 59, 59, 59, 46, 29, 46, 13, 1, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 164, 164, 164, 163, 163, 59, 59, 59, 59, 59, 59, 29, 29, 1, 59, 59] 201
rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47])
total number of confs: 839
number of broken/clashed sets: 137
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497691 none COCC(=O)N(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 3, 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]
0  hydrogens 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, 12, 11, 12, 10, 11, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 17, 59, 59, 59, 59, 59, 1, 36, 36, 36, 30, 30, 11, 11, 11, 10, 10, 2, 1, 1, 1, 1, 1, 9, 9, 59, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 229
number of broken/clashed sets: 137
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497691 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497691
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497691/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497691
Building REAL300025497692
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497692'
/scratch/stefan/7787277/working/building/REAL300025497692 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497692

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497692/0 /scratch/stefan/7787277/working/building/REAL300025497692 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 559)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/559
`/scratch/stefan/7787277/working/3D/559' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1=O)

`REAL300025497692.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497692.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497692/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497692 none CN1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 38, 129, 129, 129, 129, 129, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 1, 1, 1, 1, 1, 21, 21, 129, 1, 1, 22, 22] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44])
total number of confs: 280
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497692 none CN1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 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, 170, 170, 129, 129, 129, 129, 129, 100, 42, 100, 13, 1, 1, 1, 1, 1, 1, 1, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 170, 129, 129, 129, 129, 129, 42, 42, 1, 129, 129, 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])
total number of confs: 634
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497692 none CN1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 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, 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, 9, 9, 9, 22, 22, 22, 22, 22, 46, 46, 93, 129, 201, 201, 201, 201, 201, 22, 1, 1, 1, 2, 2, 2, 1, 1, 1, 9, 22, 22, 22, 22, 22, 93, 93, 201, 22, 22, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 43, 44, 23, 24, 25, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 543
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497692 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497692
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497692/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497692
Building REAL300025497693
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497693'
/scratch/stefan/7787277/working/building/REAL300025497693 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497693

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497693/0 /scratch/stefan/7787277/working/building/REAL300025497693 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 560)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/560
`/scratch/stefan/7787277/working/3D/560' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1=O)

`REAL300025497693.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497693.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497693/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497693 none CCN1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 5, 8, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 30, 84, 84, 84, 84, 84, 1, 16, 16, 16, 27, 27, 27, 27, 27, 16, 16, 16, 5, 1, 1, 1, 1, 1, 18, 18, 84, 1, 1, 16, 16] 201
rigid atoms, others: [45, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47])
total number of confs: 268
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497693 none CCN1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 5, 8, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 113, 113, 113, 84, 84, 84, 84, 84, 72, 38, 72, 13, 1, 1, 1, 1, 1, 1, 1, 84, 137, 137, 137, 201, 201, 201, 201, 201, 137, 137, 137, 113, 84, 84, 84, 84, 84, 38, 38, 1, 84, 84, 137, 137] 201
rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 856
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497693 none CCN1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 5, 8, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 16, 16, 16, 39, 39, 61, 81, 137, 137, 137, 137, 137, 16, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 7, 16, 16, 16, 16, 16, 61, 61, 137, 16, 16, 1, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 33, 34, 46, 47, 24, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 356
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497693 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497693
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497693/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497693
Building REAL300025497694
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497694'
/scratch/stefan/7787277/working/building/REAL300025497694 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497694

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497694/0 /scratch/stefan/7787277/working/building/REAL300025497694 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 561)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/561
`/scratch/stefan/7787277/working/3D/561' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(=O)NCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497694.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497694.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497694/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497694 none COCC(=O)NCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 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]
0  hydrogens need 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, 174, 174, 174, 167, 167, 75, 75, 75, 73, 73, 73, 73, 73, 60, 30, 60, 13, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 174, 167, 167, 167, 167, 75, 73, 73, 73, 73, 73, 30, 30, 1, 73, 73] 201
rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47])
total number of confs: 872
number of broken/clashed sets: 127
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497694 none COCC(=O)NCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 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]
0  hydrogens 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, 12, 12, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 18, 73, 73, 73, 73, 73, 1, 33, 33, 33, 29, 29, 12, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 8, 8, 73, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 229
number of broken/clashed sets: 127
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497694 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497694
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497694/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497694
Building REAL300025497695
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497695'
/scratch/stefan/7787277/working/building/REAL300025497695 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497695

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497695/0 /scratch/stefan/7787277/working/building/REAL300025497695 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 562)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/562
`/scratch/stefan/7787277/working/3D/562' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497695.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497695.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497695/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497695 none CNC(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 89, 89, 89, 65, 65, 65, 65, 65, 47, 28, 47, 13, 1, 1, 1, 1, 1, 1, 1, 65, 201, 201, 201, 201, 201, 199, 199, 89, 65, 65, 65, 65, 65, 28, 28, 1, 65, 65] 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])
total number of confs: 743
number of broken/clashed sets: 69
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497695 none CNC(=O)NCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 29, 29, 21, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 15, 65, 65, 65, 65, 65, 1, 35, 35, 35, 35, 29, 21, 21, 4, 1, 1, 1, 1, 1, 8, 8, 65, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 222
number of broken/clashed sets: 69
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497695 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497695
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497695/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497695
Building REAL300025497696
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497696'
/scratch/stefan/7787277/working/building/REAL300025497696 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497696

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497696/0 /scratch/stefan/7787277/working/building/REAL300025497696 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 563)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/563
`/scratch/stefan/7787277/working/3D/563' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=C1)

`REAL300025497696.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497696.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497696/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497696 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 24, 79, 79, 79, 79, 79, 1, 13, 13, 13, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 13, 13, 79, 1, 1, 13, 13] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43])
total number of confs: 207
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497696 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 148, 148, 105, 105, 105, 79, 79, 79, 79, 79, 53, 27, 53, 12, 1, 1, 1, 1, 1, 1, 1, 79, 148, 148, 148, 201, 201, 201, 201, 201, 105, 79, 79, 79, 79, 79, 27, 27, 1, 79, 79, 148, 148] 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: 715
number of broken/clashed sets: 40
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497696 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 1, 7, 7, 7, 7, 7, 6, 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
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, 5, 5, 5, 13, 13, 13, 13, 13, 28, 28, 55, 86, 148, 148, 148, 148, 148, 13, 1, 1, 1, 3, 3, 3, 3, 3, 5, 13, 13, 13, 13, 13, 55, 55, 148, 13, 13, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 42, 43, 23, 24, 25] set([0, 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: 373
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497696 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497696
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497696/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497696
Building REAL300025497697
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497697'
/scratch/stefan/7787277/working/building/REAL300025497697 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497697

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497697/0 /scratch/stefan/7787277/working/building/REAL300025497697 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 564)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/564
`/scratch/stefan/7787277/working/3D/564' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(C)[NH+]1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497697.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497697.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497697/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497697 none CC1CCC(C)[NH+]1CC(=O)NC1C=CCN(C(=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', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 14, 46, 46, 46, 46, 46, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 9, 9, 46, 1, 1] 63
rigid atoms, others: [45, 11, 47, 44, 43, 12, 13, 14, 15, 16, 17, 51, 52, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 122
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497697 none CC1CCC(C)[NH+]1CC(=O)NC1C=CCN(C(=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', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 63, 59, 59, 59, 46, 46, 46, 46, 46, 32, 24, 32, 12, 1, 1, 1, 1, 1, 1, 1, 46, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 59, 46, 46, 46, 46, 46, 24, 24, 1, 46, 46] 63
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: 200
number of broken/clashed sets: 63
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497697 none CC1CCC(C)[NH+]1CC(=O)NC1C=CCN(C(=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', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 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]
0  hydrogens need rotated
63  conformations in input
total number of sets (complete confs): 63
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 11, 11, 11, 11, 11, 17, 17, 32, 37, 63, 63, 63, 63, 63, 11, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 4, 11, 11, 11, 11, 11, 32, 32, 63, 11, 11] 63
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 34, 35, 36, 5, 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, 52])
total number of confs: 198
number of broken/clashed sets: 63
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497697 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497697
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497697/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497697
Building REAL300025497698
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497698'
/scratch/stefan/7787277/working/building/REAL300025497698 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497698

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497698/0 /scratch/stefan/7787277/working/building/REAL300025497698 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 565)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/565
`/scratch/stefan/7787277/working/3D/565' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCCOC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497698.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497698.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497698/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497698 none CCOCCOC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 191, 167, 146, 111, 146, 111, 111, 67, 67, 67, 67, 67, 57, 30, 56, 13, 1, 1, 1, 1, 1, 1, 1, 67, 201, 201, 201, 201, 201, 201, 201, 191, 191, 146, 146, 146, 146, 111, 67, 67, 67, 67, 67, 30, 30, 1, 67, 67] 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, 50])
total number of confs: 785
number of broken/clashed sets: 65
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497698 none CCOCCOC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens 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, 21, 17, 10, 7, 4, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 67, 67, 67, 67, 67, 1, 28, 28, 28, 28, 28, 21, 21, 17, 17, 7, 7, 7, 7, 4, 1, 1, 1, 1, 1, 9, 9, 67, 1, 1] 201
rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48])
total number of confs: 203
number of broken/clashed sets: 65
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497698 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497698
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497698/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497698
Building REAL300025497699
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497699'
/scratch/stefan/7787277/working/building/REAL300025497699 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497699

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497699/0 /scratch/stefan/7787277/working/building/REAL300025497699 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 566)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/566
`/scratch/stefan/7787277/working/3D/566' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1)

`REAL300025497699.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497699.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497699/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497699 none CN1C=C(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [57, 57, 57, 32, 26, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 22, 63, 63, 63, 63, 63, 1, 57, 57, 57, 57, 57, 57, 32, 32, 26, 26, 4, 1, 1, 1, 1, 1, 14, 14, 63, 1, 1, 57] 201
rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46])
total number of confs: 285
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497699 none CN1C=C(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 176, 172, 91, 91, 91, 63, 63, 63, 63, 63, 54, 28, 53, 13, 1, 1, 1, 1, 1, 1, 1, 63, 201, 201, 201, 201, 201, 201, 176, 176, 172, 172, 91, 63, 63, 63, 63, 63, 28, 28, 1, 63, 63, 201] 201
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46])
total number of confs: 723
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497699 none CN1C=C(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 8, 25, 25, 25, 57, 57, 57, 57, 57, 66, 66, 85, 138, 201, 201, 201, 201, 201, 57, 1, 1, 2, 2, 2, 1, 4, 4, 8, 8, 25, 57, 57, 57, 57, 57, 85, 85, 201, 57, 57, 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: 536
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497699 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497699
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497699/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497699
Building REAL300025497700
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497700'
/scratch/stefan/7787277/working/building/REAL300025497700 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497700

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497700/0 /scratch/stefan/7787277/working/building/REAL300025497700 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 567)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/567
`/scratch/stefan/7787277/working/3D/567' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC[NH+]1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497700.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497700.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497700/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497700 none O=C(CCC[NH+]1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 1, 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
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 9, 8, 10, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 9, 22, 22, 22, 22, 22, 1, 9, 9, 10, 10, 10, 9, 12, 12, 12, 12, 12, 12, 12, 12, 3, 1, 1, 1, 1, 1, 7, 7, 22, 1, 1] 29
rigid atoms, others: [45, 11, 47, 44, 43, 12, 13, 14, 15, 16, 17, 51, 52, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 98
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497700 none O=C(CCC[NH+]1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 1, 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
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [24, 24, 24, 29, 28, 29, 29, 29, 29, 29, 29, 22, 22, 22, 22, 22, 21, 18, 21, 12, 1, 1, 1, 1, 1, 1, 1, 22, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 24, 22, 22, 22, 22, 22, 18, 18, 1, 22, 22] 29
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: 102
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497700 none O=C(CCC[NH+]1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 1, 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
29  conformations in input
total number of sets (complete confs): 29
using default count positions algorithm for smaller data
unique positions, atoms: [9, 6, 5, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 12, 12, 12, 12, 12, 12, 12, 20, 22, 29, 29, 29, 29, 29, 12, 6, 6, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 9, 12, 12, 12, 12, 12, 20, 20, 29, 12, 12] 29
rigid atoms, others: [34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 41, 36, 38, 37] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 100
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497700 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497700
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497700/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497700
Building REAL300025497701
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497701'
/scratch/stefan/7787277/working/building/REAL300025497701 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497701

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497701/0 /scratch/stefan/7787277/working/building/REAL300025497701 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 568)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/568
`/scratch/stefan/7787277/working/3D/568' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)NC(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497701.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497701.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497701/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497701 none CNC(=O)NC(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 4, 7, 6, 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, 7]
0  hydrogens need rotated
201  conformations 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, 130, 198, 198, 130, 130, 79, 79, 79, 79, 79, 69, 32, 68, 13, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 198, 198, 198, 198, 198, 198, 130, 79, 79, 79, 79, 79, 32, 32, 1, 79, 79] 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])
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: REAL300025497701 none CNC(=O)NC(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 4, 7, 6, 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, 7]
0  hydrogens 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, 18, 18, 18, 15, 4, 15, 15, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 26, 79, 79, 79, 79, 79, 1, 28, 28, 28, 28, 18, 15, 15, 15, 15, 15, 15, 4, 1, 1, 1, 1, 1, 15, 15, 79, 1, 1] 201
rigid atoms, others: [48, 43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 239
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497701 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497701
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497701/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497701
Building REAL300025497702
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497702'
/scratch/stefan/7787277/working/building/REAL300025497702 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497702

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497702/0 /scratch/stefan/7787277/working/building/REAL300025497702 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 569)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/569
`/scratch/stefan/7787277/working/3D/569' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1)

`REAL300025497702.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497702.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497702/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497702 none CC1=CC=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 11, 54, 54, 54, 54, 54, 1, 39, 39, 39, 39, 39, 39, 21, 21, 4, 1, 1, 1, 1, 1, 6, 6, 54, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 177
number of broken/clashed sets: 56
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497702 none CC1=CC=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 179, 85, 85, 85, 54, 54, 54, 54, 54, 46, 30, 46, 13, 1, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 201, 201, 179, 179, 85, 54, 54, 54, 54, 54, 30, 30, 1, 54, 54] 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])
total number of confs: 763
number of broken/clashed sets: 56
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497702 none CC1=CC=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 25, 25, 25, 39, 39, 39, 39, 39, 52, 52, 88, 122, 201, 201, 201, 201, 201, 39, 1, 2, 2, 2, 1, 1, 7, 7, 25, 39, 39, 39, 39, 39, 88, 88, 201, 39, 39] 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: 556
number of broken/clashed sets: 56
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497702 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497702
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497702/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497702
Building REAL300025497703
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497703'
/scratch/stefan/7787277/working/building/REAL300025497703 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497703

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497703/0 /scratch/stefan/7787277/working/building/REAL300025497703 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 570)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/570
`/scratch/stefan/7787277/working/3D/570' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC[NH+]1CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497703.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497703.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497703/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497703 none O=C(CC[NH+]1CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 1, 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
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 10, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 12, 24, 24, 24, 24, 24, 1, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 3, 1, 1, 1, 1, 1, 8, 8, 24, 1, 1] 36
rigid atoms, others: [45, 11, 47, 44, 43, 12, 13, 14, 15, 16, 17, 51, 52, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 91
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497703 none O=C(CC[NH+]1CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 1, 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
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [25, 25, 25, 36, 36, 36, 36, 36, 36, 36, 36, 24, 24, 24, 24, 24, 20, 18, 20, 12, 1, 1, 1, 1, 1, 1, 1, 24, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 25, 24, 24, 24, 24, 24, 18, 18, 1, 24, 24] 36
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: 135
number of broken/clashed sets: 24
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497703 none O=C(CC[NH+]1CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 9, 6, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 1, 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
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 16, 16, 25, 29, 36, 36, 36, 36, 36, 11, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 25, 25, 36, 11, 11] 36
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 39, 40, 35, 41, 36, 38, 37] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 121
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497703 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497703
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497703/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497703
Building REAL300025497704
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497704'
/scratch/stefan/7787277/working/building/REAL300025497704 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497704

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497704/0 /scratch/stefan/7787277/working/building/REAL300025497704 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 571)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/571
`/scratch/stefan/7787277/working/3D/571' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1)

`REAL300025497704.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497704.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497704/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497704 none CC1=CN(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [18, 18, 18, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 34, 107, 107, 107, 107, 107, 1, 18, 18, 18, 18, 18, 18, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 18, 18, 107, 1, 1, 18] 201
rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497704 none CC1=CN(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 199, 199, 138, 138, 138, 107, 107, 107, 107, 107, 66, 30, 66, 13, 1, 1, 1, 1, 1, 1, 1, 107, 201, 201, 201, 201, 201, 201, 199, 199, 199, 199, 138, 107, 107, 107, 107, 107, 30, 30, 1, 107, 107, 201] 201
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46])
total number of confs: 690
number of broken/clashed sets: 45
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497704 none CC1=CN(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 5, 7, 10, 10, 10, 18, 18, 18, 18, 18, 42, 42, 82, 122, 201, 201, 201, 201, 201, 18, 1, 1, 2, 2, 2, 1, 5, 5, 7, 7, 10, 18, 18, 18, 18, 18, 82, 82, 201, 18, 18, 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: 545
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497704 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497704
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497704/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497704
Building REAL300025497705
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497705'
/scratch/stefan/7787277/working/building/REAL300025497705 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497705

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497705/0 /scratch/stefan/7787277/working/building/REAL300025497705 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 572)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/572
`/scratch/stefan/7787277/working/3D/572' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCS(=O)(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497705.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497705.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497705/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497705 none CCS(=O)(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 138, 138, 138, 106, 106, 106, 106, 106, 59, 29, 59, 13, 1, 1, 1, 1, 1, 1, 1, 106, 201, 201, 201, 201, 201, 201, 201, 138, 106, 106, 106, 106, 106, 29, 29, 1, 106, 106] 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])
total number of confs: 721
number of broken/clashed sets: 62
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497705 none CCS(=O)(=O)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 14, 11, 11, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens 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, 26, 19, 26, 26, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 31, 106, 106, 106, 106, 106, 1, 29, 29, 29, 29, 29, 19, 19, 5, 1, 1, 1, 1, 1, 16, 16, 106, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 308
number of broken/clashed sets: 62
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497705 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497705
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497705/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497705
Building REAL300025497706
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497706'
/scratch/stefan/7787277/working/building/REAL300025497706 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497706

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497706/0 /scratch/stefan/7787277/working/building/REAL300025497706 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 573)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/573
`/scratch/stefan/7787277/working/3D/573' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@@H+]1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497706.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497706.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497706/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497706 none CC[N@@H+]1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [9, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 11, 21, 21, 21, 21, 21, 1, 9, 9, 9, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 21, 1, 1] 23
rigid atoms, others: [45, 11, 47, 44, 43, 12, 13, 14, 15, 16, 17, 51, 52, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 77
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497706 none CC[N@@H+]1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 20, 17, 20, 12, 1, 1, 1, 1, 1, 1, 1, 21, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 21, 21, 21, 21, 21, 17, 17, 1, 21, 21] 23
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: 65
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497706 none CC[N@@H+]1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 11, 11, 16, 17, 23, 23, 23, 23, 23, 8, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 16, 16, 23, 8, 8] 23
rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 34, 40, 35, 41, 36, 38, 39, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 75
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497706 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497706/1 /scratch/stefan/7787277/working/building/REAL300025497706 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 574)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/574
`/scratch/stefan/7787277/working/3D/574' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[N@H+]1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497706.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497706.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497706/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497706 none CC[N@H+]1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [11, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 10, 16, 16, 16, 16, 16, 1, 11, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 8, 8, 16, 1, 1] 22
rigid atoms, others: [45, 11, 47, 44, 43, 12, 13, 14, 15, 16, 17, 51, 52, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 79
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497706 none CC[N@H+]1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 20, 20, 20, 16, 16, 16, 16, 16, 15, 13, 15, 11, 1, 1, 1, 1, 1, 1, 1, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 20, 16, 16, 16, 16, 16, 13, 13, 1, 16, 16] 22
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: 53
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497706 none CC[N@H+]1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 16, 16, 20, 21, 22, 22, 22, 22, 22, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 9, 9, 9, 9, 9, 20, 20, 22, 9, 9] 22
rigid atoms, others: [1, 2, 3, 4, 5, 6, 33, 8, 9, 7, 34, 40, 35, 41, 36, 38, 39, 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, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 82
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497706 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497706
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497706/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497706/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497706
Building REAL300025497707
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497707'
/scratch/stefan/7787277/working/building/REAL300025497707 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497707

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497707/0 /scratch/stefan/7787277/working/building/REAL300025497707 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 575)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/575
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)[C@H]2CCCO2)C1)

`REAL300025497707.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497707.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497707/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497707 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2CCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 32, 124, 124, 124, 124, 124, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 1, 16, 16, 124, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 17, 17, 1, 1] 201
rigid atoms, others: [32, 1, 40, 41, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 243
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497707 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2CCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 17, 47, 85, 126, 201, 201, 201, 201, 201, 17, 17, 17, 17, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 17, 85, 85, 201, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 1, 1, 17, 17] 201
rigid atoms, others: [34, 35, 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, 40, 41])
total number of confs: 517
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497707 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2CCCO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 46, 12, 1, 1, 1, 1, 1, 1, 1, 93, 124, 124, 124, 124, 124, 193, 193, 193, 201, 201, 201, 201, 201, 124, 46, 46, 1, 124, 124, 124, 124, 124, 193, 201, 201, 201, 201, 201, 201, 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, 40, 41])
total number of confs: 644
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497707 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497707
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497707/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497707
Building REAL300025497708
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497708'
/scratch/stefan/7787277/working/building/REAL300025497708 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497708

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497708/0 /scratch/stefan/7787277/working/building/REAL300025497708 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 576)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/576
`/scratch/stefan/7787277/working/3D/576' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1=O)

`REAL300025497708.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497708.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497708/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497708 none CN1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 37, 90, 90, 90, 90, 90, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 20, 21, 90, 1, 1, 21, 21, 21, 21] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47])
total number of confs: 236
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497708 none CN1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 125, 125, 125, 90, 90, 90, 90, 90, 72, 40, 72, 13, 1, 1, 1, 1, 1, 1, 1, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 125, 90, 90, 90, 90, 90, 40, 40, 1, 90, 90, 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])
total number of confs: 662
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497708 none CN1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.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, 1, 1, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 21, 21, 52, 52, 101, 137, 201, 201, 201, 201, 201, 21, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 8, 21, 21, 21, 21, 21, 101, 101, 201, 21, 21, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 32, 44, 45, 46, 47, 23, 24, 25, 26, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 568
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497708 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497708
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497708/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497708
Building REAL300025497709
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497709'
/scratch/stefan/7787277/working/building/REAL300025497709 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497709

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497709/0 /scratch/stefan/7787277/working/building/REAL300025497709 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 577)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/577
`/scratch/stefan/7787277/working/3D/577' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497709.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497709.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497709/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497709 none CCOCCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 193, 157, 112, 59, 59, 59, 59, 59, 59, 59, 59, 49, 29, 49, 13, 1, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 201, 201, 193, 193, 112, 112, 59, 59, 59, 59, 59, 59, 29, 29, 1, 59, 59] 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])
total number of confs: 740
number of broken/clashed sets: 147
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497709 none CCOCCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 37, 26, 15, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 18, 59, 59, 59, 59, 59, 1, 40, 40, 40, 40, 40, 37, 37, 26, 26, 6, 6, 2, 1, 1, 1, 1, 1, 8, 8, 59, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 253
number of broken/clashed sets: 147
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497709 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497709
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497709/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497709
Building REAL300025497710
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497710'
/scratch/stefan/7787277/working/building/REAL300025497710 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497710

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497710/0 /scratch/stefan/7787277/working/building/REAL300025497710 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 578)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/578
`/scratch/stefan/7787277/working/3D/578' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC(C1CC1)C1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497710.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497710.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497710/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025497710 none O=C(CC(C1CC1)C1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 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, 7]
0  hydrogens 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, 3, 1, 3, 4, 4, 1, 1, 1, 15, 15, 23, 23, 23, 23, 23, 27, 27, 67, 105, 201, 201, 201, 201, 201, 23, 6, 6, 3, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 15, 23, 23, 23, 23, 23, 67, 67, 201, 23, 23] 201
rigid atoms, others: [3, 36, 37, 38, 7, 8, 9, 39, 35] set([0, 1, 2, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 503
number of broken/clashed sets: 55
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL300025497710 none O=C(CC(C1CC1)C1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 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, 7]
0  hydrogens 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, 200, 201, 201, 201, 201, 201, 201, 65, 65, 65, 65, 65, 55, 26, 55, 13, 1, 1, 1, 1, 1, 1, 1, 65, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 65, 65, 65, 65, 65, 26, 26, 1, 65, 65] 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, 50])
total number of confs: 767
number of broken/clashed sets: 55
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497710 none O=C(CC(C1CC1)C1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 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, 7]
0  hydrogens 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, 15, 21, 26, 26, 21, 23, 23, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 19, 65, 65, 65, 65, 65, 1, 15, 15, 21, 26, 26, 26, 26, 26, 23, 23, 23, 23, 23, 4, 1, 1, 1, 1, 1, 10, 10, 65, 1, 1] 201
rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48])
total number of confs: 222
number of broken/clashed sets: 55
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497710 none O=C(CC(C1CC1)C1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 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, 7]
0  hydrogens 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, 3, 1, 1, 1, 1, 3, 4, 3, 17, 17, 26, 26, 26, 26, 26, 30, 30, 70, 108, 201, 201, 201, 201, 201, 26, 7, 7, 3, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 17, 26, 26, 26, 26, 26, 70, 70, 201, 26, 26] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 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, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 516
number of broken/clashed sets: 55
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497710 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497710
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497710/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497710
Building REAL300025497711
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497711'
/scratch/stefan/7787277/working/building/REAL300025497711 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497711

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497711/0 /scratch/stefan/7787277/working/building/REAL300025497711 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 579)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/579
`/scratch/stefan/7787277/working/3D/579' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1)

`REAL300025497711.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497711.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497711/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497711 none CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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, 191, 108, 108, 108, 63, 63, 63, 63, 63, 50, 30, 50, 13, 1, 1, 1, 1, 1, 1, 1, 63, 201, 201, 201, 201, 201, 201, 201, 191, 191, 108, 63, 63, 63, 63, 63, 30, 30, 1, 63, 63, 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])
total number of confs: 786
number of broken/clashed sets: 69
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497711 none CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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: [2, 1, 2, 5, 20, 20, 20, 42, 42, 42, 42, 42, 53, 53, 91, 130, 201, 201, 201, 201, 201, 42, 1, 1, 1, 2, 2, 2, 2, 5, 5, 20, 42, 42, 42, 42, 42, 91, 91, 201, 42, 42, 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: 556
number of broken/clashed sets: 69
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497711 none CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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: [42, 25, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 63, 63, 63, 63, 63, 1, 42, 42, 42, 42, 42, 42, 42, 25, 25, 5, 1, 1, 1, 1, 1, 7, 7, 63, 1, 1, 42, 42, 42, 42, 42] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 41] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46])
total number of confs: 273
number of broken/clashed sets: 69
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497711 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497711
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497711/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497711
Building REAL300025497712
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497712'
/scratch/stefan/7787277/working/building/REAL300025497712 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497712

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497712/0 /scratch/stefan/7787277/working/building/REAL300025497712 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 580)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/580
`/scratch/stefan/7787277/working/3D/580' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3CCC2CC3)C1)

`REAL300025497712.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497712.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497712/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497712 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3CCC2CC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [6, 1, 6, 18, 38, 140, 140, 140, 140, 140, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 1, 18, 18, 139, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 49, 50, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 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])
total number of confs: 266
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497712 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3CCC2CC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [37, 15, 37, 74, 120, 201, 201, 201, 201, 201, 15, 15, 15, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 15, 74, 74, 201, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 201
rigid atoms, others: [16, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 49, 50])
total number of confs: 480
number of broken/clashed sets: 36
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497712 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3CCC2CC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [102, 48, 13, 1, 1, 1, 1, 1, 1, 1, 102, 140, 140, 140, 140, 140, 187, 187, 187, 201, 201, 201, 201, 201, 201, 201, 140, 48, 48, 1, 140, 140, 140, 140, 140, 187, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 140] 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: 613
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497712 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497712
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497712/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497712
Building REAL300025497713
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497713'
/scratch/stefan/7787277/working/building/REAL300025497713 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497713

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497713/0 /scratch/stefan/7787277/working/building/REAL300025497713 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 581)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/581
`/scratch/stefan/7787277/working/3D/581' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C)

`REAL300025497713.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497713.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497713/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497713 none CCCCC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [200, 200, 198, 194, 104, 104, 104, 59, 59, 59, 59, 59, 44, 29, 44, 13, 1, 1, 1, 1, 1, 1, 1, 59, 194, 199, 196, 200, 200, 200, 200, 200, 200, 200, 198, 198, 194, 104, 59, 59, 59, 59, 59, 29, 29, 1, 59, 59, 199, 199, 199, 199, 199, 199, 199] 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: 840
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: REAL300025497713 none CCCCC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 20, 18, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 59, 59, 59, 59, 59, 1, 14, 19, 18, 21, 21, 21, 21, 21, 20, 20, 18, 18, 14, 5, 1, 1, 1, 1, 1, 10, 10, 59, 1, 1, 19, 19, 19, 19, 19, 19, 19] 201
rigid atoms, others: [11, 38, 7, 8, 9, 10, 39, 12, 13, 46, 47, 40, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 226
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497713 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497713
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497713/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497713
Building REAL300025497714
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497714'
/scratch/stefan/7787277/working/building/REAL300025497714 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497714

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497714/0 /scratch/stefan/7787277/working/building/REAL300025497714 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 582)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/582
`/scratch/stefan/7787277/working/3D/582' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1)

`REAL300025497714.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497714.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497714/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497714 none CC1=NC=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens 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, 20, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 46, 46, 46, 46, 46, 1, 40, 40, 40, 40, 40, 20, 20, 4, 1, 1, 1, 1, 1, 5, 5, 46, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 168
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497714 none CC1=NC=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 176, 76, 76, 76, 46, 46, 46, 46, 46, 40, 28, 40, 13, 1, 1, 1, 1, 1, 1, 1, 46, 201, 201, 201, 201, 201, 176, 176, 76, 46, 46, 46, 46, 46, 28, 28, 1, 46, 46] 201
rigid atoms, others: [40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42])
total number of confs: 749
number of broken/clashed sets: 52
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497714 none CC1=NC=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
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, 23, 23, 23, 40, 40, 40, 40, 40, 46, 46, 85, 125, 201, 201, 201, 201, 201, 40, 1, 2, 2, 2, 1, 7, 7, 23, 40, 40, 40, 40, 40, 85, 85, 201, 40, 40] 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: 554
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497714 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497714
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497714/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497714
Building REAL300025497715
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497715'
/scratch/stefan/7787277/working/building/REAL300025497715 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497715

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497715/0 /scratch/stefan/7787277/working/building/REAL300025497715 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 583)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/583
`/scratch/stefan/7787277/working/3D/583' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C)

`REAL300025497715.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497715.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497715/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497715 none CCOC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 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, 7, 7]
0  hydrogens 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, 199, 197, 195, 117, 117, 117, 79, 79, 79, 79, 79, 57, 29, 57, 13, 1, 1, 1, 1, 1, 1, 1, 79, 193, 201, 201, 199, 199, 199, 199, 199, 197, 195, 195, 117, 79, 79, 79, 79, 79, 29, 29, 1, 79, 79, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 825
number of broken/clashed sets: 93
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497715 none CCOC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 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, 7, 7]
0  hydrogens 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, 27, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 18, 79, 79, 79, 79, 79, 1, 25, 34, 34, 28, 28, 28, 28, 28, 27, 19, 19, 4, 1, 1, 1, 1, 1, 9, 9, 79, 1, 1, 33, 34, 34, 34, 34, 34, 34] 201
rigid atoms, others: [45, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 270
number of broken/clashed sets: 93
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497715 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497715
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497715/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497715
Building REAL300025497716
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497716'
/scratch/stefan/7787277/working/building/REAL300025497716 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497716

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497716/0 /scratch/stefan/7787277/working/building/REAL300025497716 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 584)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/584
`/scratch/stefan/7787277/working/3D/584' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)C1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1)

`REAL300025497716.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497716.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497716/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497716 none C[NH+](C)C1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [6, 5, 6, 6, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 1, 5, 5, 5, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5] 8
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49])
total number of confs: 32
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497716 none C[NH+](C)C1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 8, 8, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 4, 4, 4, 4, 4, 4, 4, 1, 4, 4, 8, 8, 8, 8, 8, 8] 8
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 21
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497716 none C[NH+](C)C1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 9, 6, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 3, 1, 1, 3, 3, 3, 5, 5, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1] 8
rigid atoms, others: [1, 4, 5, 44, 45, 46, 47, 48, 49, 24, 25, 26] set([0, 2, 3, 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])
total number of confs: 36
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497716 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497716
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497716/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497716
Building REAL300025497717
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497717'
/scratch/stefan/7787277/working/building/REAL300025497717 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497717

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497717/0 /scratch/stefan/7787277/working/building/REAL300025497717 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 585)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/585
`/scratch/stefan/7787277/working/3D/585' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CSC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497717.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497717.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497717/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497717 none O=C(CCC1=CSC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 1, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 19, 22, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 11, 42, 42, 42, 42, 42, 1, 19, 19, 22, 22, 40, 40, 40, 5, 1, 1, 1, 1, 1, 6, 6, 42, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 183
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497717 none O=C(CCC1=CSC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 1, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 107, 121, 201, 201, 201, 201, 42, 42, 42, 42, 42, 35, 25, 35, 13, 1, 1, 1, 1, 1, 1, 1, 42, 107, 107, 121, 121, 201, 201, 201, 62, 42, 42, 42, 42, 42, 25, 25, 1, 42, 42] 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])
total number of confs: 644
number of broken/clashed sets: 53
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497717 none O=C(CCC1=CSC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 1, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 2, 1, 1, 1, 1, 1, 1, 23, 23, 40, 40, 40, 40, 40, 48, 48, 91, 131, 201, 201, 201, 201, 201, 40, 6, 6, 2, 2, 1, 1, 1, 23, 40, 40, 40, 40, 40, 91, 91, 201, 40, 40] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 578
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497717 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497717
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497717/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497717
Building REAL300025497718
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497718'
/scratch/stefan/7787277/working/building/REAL300025497718 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497718

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497718/0 /scratch/stefan/7787277/working/building/REAL300025497718 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 586)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/586
`/scratch/stefan/7787277/working/3D/586' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)C(F)=C2)C1)

`REAL300025497718.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497718.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497718/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497718 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)C(F)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 15, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 1, 13, 13, 55, 1, 1, 1, 1, 1, 5, 14, 14, 14, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 10, 11, 12, 13, 14, 15, 39, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38])
total number of confs: 135
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497718 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)C(F)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 15, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 14, 37, 76, 107, 201, 201, 201, 201, 201, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 14, 76, 76, 201, 14, 14, 14, 14, 14, 5, 1, 1, 1, 14, 14] 201
rigid atoms, others: [36, 37, 38, 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, 39, 40])
total number of confs: 503
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497718 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)C(F)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'F', 'C.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 15, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 30, 13, 1, 1, 1, 1, 1, 1, 1, 41, 55, 55, 55, 55, 55, 76, 76, 76, 201, 201, 201, 201, 201, 201, 201, 55, 30, 30, 1, 55, 55, 55, 55, 55, 76, 201, 201, 201, 55, 55] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 427
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497718 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497718
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497718/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497718
Building REAL300025497719
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497719'
/scratch/stefan/7787277/working/building/REAL300025497719 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497719

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497719/0 /scratch/stefan/7787277/working/building/REAL300025497719 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 587)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/587
`/scratch/stefan/7787277/working/3D/587' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(F)=CC=C2F)C1)

`REAL300025497719.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497719.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497719/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497719 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(F)=CC=C2F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 18, 38, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 1, 18, 18, 125, 1, 1, 1, 1, 1, 5, 15, 7, 15, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 10, 11, 12, 13, 14, 15, 39, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38])
total number of confs: 243
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497719 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(F)=CC=C2F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 15, 36, 71, 106, 201, 201, 201, 201, 201, 15, 15, 15, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 71, 71, 201, 15, 15, 15, 15, 15, 8, 1, 1, 1, 15, 15] 201
rigid atoms, others: [36, 37, 38, 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, 39, 40])
total number of confs: 474
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497719 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(F)=CC=C2F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 15, 1, 1, 1, 15, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 44, 13, 1, 1, 1, 1, 1, 1, 1, 90, 125, 125, 125, 125, 125, 188, 188, 188, 201, 201, 201, 201, 201, 201, 201, 125, 44, 44, 1, 125, 125, 125, 125, 125, 188, 201, 201, 201, 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])
total number of confs: 601
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497719 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497719
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497719/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497719
Building REAL300025497720
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497720'
/scratch/stefan/7787277/working/building/REAL300025497720 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497720

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497720/0 /scratch/stefan/7787277/working/building/REAL300025497720 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 588)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/588
`/scratch/stefan/7787277/working/3D/588' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(OCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1)

`REAL300025497720.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497720.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497720/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497720 none CC1=CC(OCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 34, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 23, 89, 89, 89, 89, 89, 1, 39, 39, 39, 39, 39, 39, 19, 19, 4, 1, 1, 1, 1, 1, 11, 11, 89, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 232
number of broken/clashed sets: 46
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497720 none CC1=CC(OCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 128, 128, 128, 89, 89, 89, 89, 89, 75, 31, 75, 13, 1, 1, 1, 1, 1, 1, 1, 89, 201, 201, 201, 201, 201, 201, 195, 195, 128, 89, 89, 89, 89, 89, 31, 31, 1, 89, 89] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43])
total number of confs: 737
number of broken/clashed sets: 46
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497720 none CC1=CC(OCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 11, 28, 28, 28, 39, 39, 39, 39, 39, 43, 43, 88, 129, 201, 201, 201, 201, 201, 39, 1, 1, 2, 2, 2, 1, 11, 11, 28, 39, 39, 39, 39, 39, 88, 88, 201, 39, 39] 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])
total number of confs: 546
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497720 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497720
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497720/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497720
Building REAL300025497721
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497721'
/scratch/stefan/7787277/working/building/REAL300025497721 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497721

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497721/0 /scratch/stefan/7787277/working/building/REAL300025497721 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 589)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/589
`/scratch/stefan/7787277/working/3D/589' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C(N)=O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497721.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497721.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497721/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497721 none CC(C)(C(N)=O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [13, 5, 13, 13, 15, 15, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 13, 13, 15, 15, 5, 4, 4, 4, 4, 4, 4, 4, 1, 4, 4] 15
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])
total number of confs: 58
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: REAL300025497721 none CC(C)(C(N)=O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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, 4, 11, 11, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 1, 11, 11, 11, 11, 11, 11, 13, 13, 4, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1] 15
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 59
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497721 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497721
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497721/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497721
Building REAL300025497722
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497722'
/scratch/stefan/7787277/working/building/REAL300025497722 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497722

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497722/0 /scratch/stefan/7787277/working/building/REAL300025497722 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 590)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/590
`/scratch/stefan/7787277/working/3D/590' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)[C@@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C)

`REAL300025497722.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497722.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497722/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497722 none CC(C)[C@@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
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: [56, 69, 69, 55, 69, 55, 55, 29, 29, 29, 29, 29, 29, 23, 29, 12, 1, 1, 1, 1, 1, 1, 1, 29, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 55, 29, 29, 29, 29, 29, 23, 23, 1, 29, 29, 69, 69, 69, 69, 69, 69] 69
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])
total number of confs: 348
number of broken/clashed sets: 68
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497722 none CC(C)[C@@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 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]
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: [8, 11, 12, 5, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 10, 29, 29, 29, 29, 29, 1, 11, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 8, 8, 29, 1, 1, 13, 13, 13, 13, 13, 13] 69
rigid atoms, others: [45, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49, 50, 51])
total number of confs: 146
number of broken/clashed sets: 68
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497722 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497722
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497722/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497722
Building REAL300025497723
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497723'
/scratch/stefan/7787277/working/building/REAL300025497723 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497723

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497723/0 /scratch/stefan/7787277/working/building/REAL300025497723 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 591)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/591
`/scratch/stefan/7787277/working/3D/591' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C=N1)

`REAL300025497723.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497723.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497723/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497723 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 8, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 32, 91, 91, 91, 91, 91, 1, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 14, 14, 91, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 21, 39, 38, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43])
total number of confs: 180
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497723 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 8, 7, 7, 7, 6, 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]
0  hydrogens need rotated
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, 91, 91, 91, 91, 91, 76, 39, 76, 13, 1, 1, 1, 1, 1, 1, 1, 91, 201, 201, 201, 201, 201, 201, 201, 115, 91, 91, 91, 91, 91, 39, 39, 1, 91, 91, 201, 201, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 524
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497723 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 8, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 13, 13, 13, 13, 13, 31, 31, 62, 103, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 2, 2, 2, 6, 13, 13, 13, 13, 13, 62, 62, 201, 13, 13, 2, 2, 2, 1] 201
rigid atoms, others: [0, 1, 2, 3, 43, 22, 23, 24, 25] set([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: 478
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497723 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497723
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497723/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497723
Building REAL300025497724
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497724'
/scratch/stefan/7787277/working/building/REAL300025497724 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497724

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497724/0 /scratch/stefan/7787277/working/building/REAL300025497724 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 592)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/592
`/scratch/stefan/7787277/working/3D/592' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3C=CNC3=N2)C1)

`REAL300025497724.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497724.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497724/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497724 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3C=CNC3=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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, 30, 54, 146, 146, 146, 146, 146, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 1, 30, 30, 146, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 300
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497724 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3C=CNC3=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 11, 31, 82, 119, 201, 201, 201, 201, 201, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 82, 82, 201, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 11, 11] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 523
number of broken/clashed sets: 24
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497724 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3C=CNC3=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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: [103, 45, 13, 1, 1, 1, 1, 1, 1, 1, 103, 146, 146, 146, 146, 146, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 146, 45, 45, 1, 146, 146, 146, 146, 146, 200, 201, 201, 201, 201, 201, 146, 146] 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: 598
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497724 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497724
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497724/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497724
Building REAL300025497725
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497725'
/scratch/stefan/7787277/working/building/REAL300025497725 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497725

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497725/0 /scratch/stefan/7787277/working/building/REAL300025497725 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 593)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/593
`/scratch/stefan/7787277/working/3D/593' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3NC=CC3=C2)C1)

`REAL300025497725.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497725.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497725/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497725 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3NC=CC3=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 7, 7, 6, 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, 3, 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: [5, 1, 5, 15, 31, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 12, 1, 15, 15, 105, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 202
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497725 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3NC=CC3=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 7, 7, 6, 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, 3, 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: [33, 12, 33, 64, 107, 201, 201, 201, 201, 201, 12, 12, 12, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 64, 64, 201, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 12, 12] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 482
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497725 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3NC=CC3=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 7, 7, 6, 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, 3, 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: [82, 49, 13, 1, 1, 1, 1, 1, 1, 1, 82, 105, 105, 105, 105, 105, 129, 129, 129, 201, 201, 201, 201, 201, 201, 201, 201, 105, 49, 49, 1, 105, 105, 105, 105, 105, 129, 201, 201, 201, 201, 201, 105, 105] 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: 529
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497725 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497725
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497725/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497725
Building REAL300025497726
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497726'
/scratch/stefan/7787277/working/building/REAL300025497726 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497726

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497726/0 /scratch/stefan/7787277/working/building/REAL300025497726 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 594)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/594
`/scratch/stefan/7787277/working/3D/594' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CN=CS1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497726.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497726.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497726/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497726 none O=C(CC1=CN=CS1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 14, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 22, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 19, 82, 82, 82, 82, 82, 1, 22, 22, 35, 35, 5, 1, 1, 1, 1, 1, 11, 11, 82, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 39, 8, 9, 10, 11, 12, 13, 14, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 226
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497726 none O=C(CC1=CN=CS1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 14, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 107, 107, 177, 201, 201, 201, 201, 82, 82, 82, 82, 82, 52, 28, 52, 13, 1, 1, 1, 1, 1, 1, 1, 82, 177, 177, 201, 201, 107, 82, 82, 82, 82, 82, 28, 28, 1, 82, 82] 201
rigid atoms, others: [37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 688
number of broken/clashed sets: 45
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497726 none O=C(CC1=CN=CS1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 14, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 4, 1, 1, 1, 1, 1, 1, 23, 23, 35, 35, 35, 35, 35, 51, 51, 85, 125, 201, 201, 201, 201, 201, 35, 4, 4, 1, 1, 23, 35, 35, 35, 35, 35, 85, 85, 201, 35, 35] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 540
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497726 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497726
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497726/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497726
Building REAL300025497727
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497727'
/scratch/stefan/7787277/working/building/REAL300025497727 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497727

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497727/0 /scratch/stefan/7787277/working/building/REAL300025497727 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 595)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/595
`/scratch/stefan/7787277/working/3D/595' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(=O)NN=C2)C1)

`REAL300025497727.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497727.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497727/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497727 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(=O)NN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 5, 7, 7, 6, 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, 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: [5, 1, 5, 14, 29, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 1, 14, 14, 101, 1, 1, 1, 1, 1, 5, 11, 11, 11, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37])
total number of confs: 192
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497727 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(=O)NN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 5, 7, 7, 6, 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, 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: [28, 11, 28, 64, 99, 201, 201, 201, 201, 201, 11, 11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 64, 64, 201, 11, 11, 11, 11, 11, 5, 1, 1, 1, 11, 11] 201
rigid atoms, others: [35, 36, 37, 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, 38, 39])
total number of confs: 470
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497727 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC(=O)NN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'N.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 11, 8, 8, 1, 5, 7, 7, 6, 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, 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: [71, 46, 13, 1, 1, 1, 1, 1, 1, 1, 71, 101, 101, 101, 101, 101, 129, 129, 129, 201, 201, 201, 201, 201, 201, 101, 46, 46, 1, 101, 101, 101, 101, 101, 129, 201, 201, 201, 101, 101] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 521
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497727 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497727
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497727/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497727
Building REAL300025497728
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497728'
/scratch/stefan/7787277/working/building/REAL300025497728 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497728

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497728/0 /scratch/stefan/7787277/working/building/REAL300025497728 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 596)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/596
`/scratch/stefan/7787277/working/3D/596' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)NC(=O)N1)

`REAL300025497728.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497728.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497728/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497728 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)NC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 28, 84, 84, 84, 84, 84, 1, 20, 20, 20, 20, 20, 20, 20, 4, 1, 1, 1, 1, 1, 12, 12, 84, 1, 1, 20, 20] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 21, 39, 38, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41])
total number of confs: 163
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497728 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)NC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 132, 132, 132, 84, 84, 84, 84, 84, 75, 48, 75, 13, 1, 1, 1, 1, 1, 1, 1, 84, 201, 201, 201, 201, 201, 201, 201, 132, 84, 84, 84, 84, 84, 48, 48, 1, 84, 84, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 551
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497728 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)NC(=O)N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.am', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 20, 20, 20, 20, 20, 42, 42, 74, 108, 201, 201, 201, 201, 201, 20, 1, 1, 1, 1, 2, 2, 2, 9, 20, 20, 20, 20, 20, 74, 74, 201, 20, 20, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 40, 41, 22, 23, 24, 25] set([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])
total number of confs: 488
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497728 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497728
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497728/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497728
Building REAL300025497729
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497729'
/scratch/stefan/7787277/working/building/REAL300025497729 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497729

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497729/0 /scratch/stefan/7787277/working/building/REAL300025497729 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 597)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/597
`/scratch/stefan/7787277/working/3D/597' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC=C2Cl)C1)

`REAL300025497729.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497729.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497729/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497729 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 14, 1, 1, 16, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 14, 28, 90, 90, 90, 90, 90, 1, 1, 1, 1, 1, 1, 4, 4, 4, 14, 14, 14, 14, 14, 1, 14, 14, 90, 1, 1, 1, 1, 1, 4, 14, 14, 1, 1] 201
rigid atoms, others: [32, 1, 36, 37, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35])
total number of confs: 177
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497729 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 14, 1, 1, 16, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 14, 31, 63, 103, 201, 201, 201, 201, 201, 14, 14, 14, 14, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 14, 63, 63, 201, 14, 14, 14, 14, 14, 6, 1, 1, 14, 14] 201
rigid atoms, others: [34, 35, 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, 36, 37])
total number of confs: 469
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497729 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 14, 1, 1, 16, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [71, 44, 13, 1, 1, 1, 1, 1, 1, 1, 71, 90, 90, 90, 90, 90, 121, 121, 121, 201, 201, 201, 201, 201, 90, 44, 44, 1, 90, 90, 90, 90, 90, 121, 201, 201, 90, 90] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 518
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497729 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497729
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497729/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497729
Building REAL300025497730
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497730'
/scratch/stefan/7787277/working/building/REAL300025497730 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497730

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497730/0 /scratch/stefan/7787277/working/building/REAL300025497730 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 598)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/598
`/scratch/stefan/7787277/working/3D/598' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NN(C)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497730.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497730.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497730/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497730 none CCC1=NN(C)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens 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, 12, 12, 12, 12, 12, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 24, 100, 100, 100, 100, 100, 1, 28, 28, 28, 28, 28, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 14, 14, 100, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 260
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497730 none CCC1=NN(C)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 164, 164, 164, 164, 164, 164, 147, 147, 147, 100, 100, 100, 100, 100, 72, 30, 72, 13, 1, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 201, 164, 164, 164, 164, 147, 100, 100, 100, 100, 100, 30, 30, 1, 100, 100] 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])
total number of confs: 708
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497730 none CCC1=NN(C)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 24, 24, 49, 79, 164, 164, 164, 164, 164, 12, 6, 6, 6, 5, 5, 2, 2, 2, 1, 5, 12, 12, 12, 12, 12, 49, 49, 164, 12, 12] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 35] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 395
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497730 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497730
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497730/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497730
Building REAL300025497731
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497731'
/scratch/stefan/7787277/working/building/REAL300025497731 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497731

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497731/0 /scratch/stefan/7787277/working/building/REAL300025497731 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 599)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/599
`/scratch/stefan/7787277/working/3D/599' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C3CC3)CC2)C1)

`REAL300025497731.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497731.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497731/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025497731 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C3CC3)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 8, 14, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 35, 35, 11, 11, 1, 8, 8, 54, 1, 1, 1, 1, 1, 4, 35, 35, 35, 35, 35, 11, 11, 11, 11, 1, 1] 201
rigid atoms, others: [32, 1, 43, 44, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 181
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.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: REAL300025497731 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C3CC3)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 36, 57, 85, 115, 201, 201, 201, 201, 201, 36, 36, 36, 36, 19, 19, 10, 19, 1, 1, 1, 1, 10, 10, 36, 85, 85, 201, 36, 36, 36, 36, 36, 19, 1, 1, 1, 1, 1, 10, 10, 10, 10, 36, 36] 201
rigid atoms, others: [34, 35, 36, 37, 38, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 42, 43, 44])
total number of confs: 520
number of broken/clashed sets: 27
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497731 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C3CC3)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 41, 61, 141, 141, 141, 141, 141, 11, 11, 11, 11, 5, 5, 1, 5, 1, 1, 9, 9, 1, 1, 11, 41, 41, 141, 11, 11, 11, 11, 11, 5, 9, 9, 9, 9, 9, 1, 1, 1, 1, 11, 11] 201
rigid atoms, others: [39, 40, 41, 42, 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, 43, 44])
total number of confs: 331
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497731 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C3CC3)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 23, 12, 1, 1, 1, 1, 1, 1, 1, 40, 54, 54, 54, 54, 54, 84, 84, 84, 141, 201, 201, 141, 141, 54, 23, 23, 1, 54, 54, 54, 54, 54, 84, 201, 201, 201, 201, 201, 141, 141, 141, 141, 54, 54] 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: 718
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497731 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497731
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497731/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497731
Building REAL300025497732
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497732'
/scratch/stefan/7787277/working/building/REAL300025497732 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497732

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497732/0 /scratch/stefan/7787277/working/building/REAL300025497732 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 600)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/600
`/scratch/stefan/7787277/working/3D/600' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497732.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497732.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497732/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497732 none COC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [33, 22, 22, 22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 29, 78, 78, 78, 78, 78, 1, 22, 33, 33, 33, 22, 22, 22, 22, 5, 1, 1, 1, 1, 1, 16, 16, 78, 1, 1, 22, 22] 201
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44])
total number of confs: 229
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497732 none COC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 92, 92, 92, 78, 78, 78, 78, 78, 69, 38, 69, 13, 1, 1, 1, 1, 1, 1, 1, 78, 201, 201, 201, 201, 201, 201, 201, 201, 92, 78, 78, 78, 78, 78, 38, 38, 1, 78, 78, 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])
total number of confs: 635
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497732 none COC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', '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, 1, 1, 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, 6, 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]
0  hydrogens 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, 11, 11, 11, 22, 22, 22, 22, 22, 45, 45, 74, 113, 201, 201, 201, 201, 201, 22, 1, 5, 5, 5, 1, 1, 1, 1, 11, 22, 22, 22, 22, 22, 74, 74, 201, 22, 22, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 43, 44, 24, 28, 29, 30, 31] set([0, 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])
total number of confs: 495
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497732 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497732
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497732/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497732
Building REAL300025497733
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497733'
/scratch/stefan/7787277/working/building/REAL300025497733 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497733

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497733/0 /scratch/stefan/7787277/working/building/REAL300025497733 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 601)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/601
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)[C@H]2CCCC(=O)N2)C1)

`REAL300025497733.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497733.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497733/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497733 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2CCCC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 17, 35, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 1, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 1, 17, 17, 112, 1, 1, 1, 1, 1, 5, 21, 21, 21, 21, 21, 21, 21, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 44, 10, 11, 12, 13, 14, 15, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 243
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497733 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2CCCC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 21, 41, 77, 110, 201, 201, 201, 201, 201, 21, 21, 21, 21, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 21, 77, 77, 201, 21, 21, 21, 21, 21, 11, 1, 1, 1, 1, 1, 1, 1, 21, 21] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 16, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44])
total number of confs: 486
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497733 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2CCCC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [81, 42, 12, 1, 1, 1, 1, 1, 1, 1, 81, 112, 112, 112, 112, 112, 152, 152, 152, 201, 201, 201, 201, 201, 201, 201, 112, 42, 42, 1, 112, 112, 112, 112, 112, 152, 201, 201, 201, 201, 201, 201, 201, 112, 112] 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: 627
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497733 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497733
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497733/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497733
Building REAL300025497734
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497734'
/scratch/stefan/7787277/working/building/REAL300025497734 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497734

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497734/0 /scratch/stefan/7787277/working/building/REAL300025497734 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 602)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/602
`/scratch/stefan/7787277/working/3D/602' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O)

`REAL300025497734.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497734.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497734/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497734 none CN1CCC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7, 7]
0  hydrogens 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, 18, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 32, 100, 100, 100, 100, 100, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 18, 18, 5, 1, 1, 1, 1, 1, 16, 16, 100, 1, 1] 201
rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 40, 46, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 260
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497734 none CN1CCC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 149, 149, 149, 100, 100, 100, 100, 100, 62, 28, 62, 13, 1, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 100, 100, 100, 100, 100, 28, 28, 1, 100, 100] 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: 683
number of broken/clashed sets: 52
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497734 none CN1CCC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 15, 15, 15, 25, 25, 25, 25, 25, 51, 51, 86, 125, 201, 201, 201, 201, 201, 25, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 7, 7, 15, 25, 25, 25, 25, 25, 86, 86, 201, 25, 25] 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: 534
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497734 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497734
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497734/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497734
Building REAL300025497735
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497735'
/scratch/stefan/7787277/working/building/REAL300025497735 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497735

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497735/0 /scratch/stefan/7787277/working/building/REAL300025497735 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 603)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/603
`/scratch/stefan/7787277/working/3D/603' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1)

`REAL300025497735.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497735.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497735/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497735 none COCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 7, 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: [25, 16, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 30, 78, 78, 78, 78, 78, 1, 7, 7, 7, 7, 25, 25, 25, 16, 16, 4, 1, 1, 1, 1, 1, 16, 16, 78, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 227
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497735 none COCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 7, 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, 175, 136, 136, 136, 78, 78, 78, 78, 78, 60, 28, 60, 13, 1, 1, 1, 1, 1, 1, 1, 78, 175, 175, 175, 175, 201, 201, 201, 201, 201, 136, 78, 78, 78, 78, 78, 28, 28, 1, 78, 78, 175, 175, 175, 175, 175, 175, 175, 175] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 707
number of broken/clashed sets: 31
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497735 none COCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 7, 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: [12, 6, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 22, 22, 55, 88, 175, 175, 175, 175, 175, 7, 1, 1, 1, 1, 12, 12, 12, 6, 6, 3, 7, 7, 7, 7, 7, 55, 55, 175, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 3, 4, 43, 44, 45, 46, 47, 48, 49, 50, 23, 24, 25, 26] set([0, 1, 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: 442
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497735 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497735
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497735/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497735
Building REAL300025497736
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497736'
/scratch/stefan/7787277/working/building/REAL300025497736 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497736

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497736/0 /scratch/stefan/7787277/working/building/REAL300025497736 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 604)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/604
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2=NN3CCCC3=C2)C1)

`REAL300025497736.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497736.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497736/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497736 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NN3CCCC3=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 5, 5, 5, 1, 1, 5, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 28, 57, 152, 152, 152, 152, 152, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 1, 28, 28, 152, 1, 1, 1, 1, 1, 6, 12, 12, 12, 12, 12, 12, 12, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 44, 10, 11, 12, 13, 14, 15, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 301
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497736 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NN3CCCC3=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 5, 5, 5, 1, 1, 5, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 12, 35, 86, 126, 201, 201, 201, 201, 201, 12, 12, 12, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 86, 86, 201, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 16, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44])
total number of confs: 516
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497736 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NN3CCCC3=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 5, 5, 5, 1, 1, 5, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [114, 44, 13, 1, 1, 1, 1, 1, 1, 1, 114, 152, 152, 152, 152, 152, 198, 198, 198, 201, 201, 201, 201, 201, 201, 201, 152, 44, 44, 1, 152, 152, 152, 152, 152, 198, 201, 201, 201, 201, 201, 201, 201, 152, 152] 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: 608
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497736 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497736
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497736/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497736
Building REAL300025497737
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497737'
/scratch/stefan/7787277/working/building/REAL300025497737 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497737

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497737/0 /scratch/stefan/7787277/working/building/REAL300025497737 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 605)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/605
`/scratch/stefan/7787277/working/3D/605' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=N1)

`REAL300025497737.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497737.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497737/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497737 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 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: [33, 17, 17, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 27, 105, 105, 105, 105, 105, 1, 17, 17, 17, 33, 33, 33, 33, 33, 4, 1, 1, 1, 1, 1, 14, 14, 105, 1, 1, 17] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42])
total number of confs: 279
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497737 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 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, 199, 199, 140, 140, 140, 105, 105, 105, 105, 105, 75, 30, 75, 13, 1, 1, 1, 1, 1, 1, 1, 105, 199, 199, 199, 201, 201, 201, 201, 201, 140, 105, 105, 105, 105, 105, 30, 30, 1, 105, 105, 199] 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: 533
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497737 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 8, 7, 7, 7, 7, 7, 6, 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: [5, 1, 1, 1, 1, 8, 8, 8, 17, 17, 17, 17, 17, 33, 33, 72, 109, 199, 199, 199, 199, 199, 17, 1, 1, 1, 5, 5, 5, 5, 5, 8, 17, 17, 17, 17, 17, 72, 72, 199, 17, 17, 1] 201
rigid atoms, others: [1, 2, 3, 4, 42, 23, 24, 25] set([0, 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: 498
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497737 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497737
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497737/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497737
Building REAL300025497738
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497738'
/scratch/stefan/7787277/working/building/REAL300025497738 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497738

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497738/0 /scratch/stefan/7787277/working/building/REAL300025497738 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 606)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/606
`/scratch/stefan/7787277/working/3D/606' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3CCCN3N=C2)C1)

`REAL300025497738.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497738.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497738/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497738 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3CCCN3N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 8, 1, 5, 7, 7, 6, 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]
0  hydrogens 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, 33, 98, 98, 98, 98, 98, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 1, 16, 16, 98, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 44, 10, 11, 12, 13, 14, 15, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 201
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497738 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3CCCN3N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 8, 1, 5, 7, 7, 6, 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]
0  hydrogens 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, 18, 41, 76, 113, 201, 201, 201, 201, 201, 18, 18, 18, 18, 7, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 18, 76, 76, 201, 18, 18, 18, 18, 18, 7, 1, 1, 1, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 16, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44])
total number of confs: 492
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497738 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3CCCN3N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 8, 8, 1, 5, 7, 7, 6, 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]
0  hydrogens 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, 36, 13, 1, 1, 1, 1, 1, 1, 1, 70, 98, 98, 98, 98, 98, 146, 146, 146, 201, 201, 201, 201, 201, 201, 201, 98, 36, 36, 1, 98, 98, 98, 98, 98, 146, 201, 201, 201, 201, 201, 201, 201, 98, 98] 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: 561
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497738 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497738
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497738/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497738
Building REAL300025497739
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497739'
/scratch/stefan/7787277/working/building/REAL300025497739 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497739

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497739/0 /scratch/stefan/7787277/working/building/REAL300025497739 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 607)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/607
`/scratch/stefan/7787277/working/3D/607' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC(F)(F)C2)C1)

`REAL300025497739.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497739.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497739/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497739 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC(F)(F)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 22, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 19, 19, 19, 1, 13, 13, 68, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [32, 1, 43, 33, 10, 11, 12, 13, 14, 15, 42, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 170
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497739 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC(F)(F)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 19, 41, 74, 100, 201, 201, 201, 201, 201, 19, 19, 19, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 19, 74, 74, 201, 19, 19, 19, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [35, 36, 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, 42, 43])
total number of confs: 495
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497739 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC(F)(F)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 32, 12, 1, 1, 1, 1, 1, 1, 1, 48, 68, 68, 68, 68, 68, 102, 102, 102, 201, 201, 201, 201, 201, 201, 68, 32, 32, 1, 68, 68, 68, 68, 68, 102, 201, 201, 201, 201, 201, 201, 201, 68, 68] 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: 624
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497739 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497739
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497739/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497739
Building REAL300025497740
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497740'
/scratch/stefan/7787277/working/building/REAL300025497740 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497740

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497740/0 /scratch/stefan/7787277/working/building/REAL300025497740 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 608)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/608
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2(F)CCOCC2)C1)

`REAL300025497740.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497740.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497740/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497740 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(F)CCOCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 7, 7, 6, 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: [5, 1, 5, 13, 29, 103, 102, 103, 103, 103, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 19, 19, 19, 1, 14, 13, 103, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [32, 1, 43, 33, 44, 10, 11, 12, 13, 14, 15, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 222
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497740 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(F)CCOCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 7, 7, 6, 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: [40, 19, 40, 86, 124, 201, 201, 201, 201, 201, 19, 19, 19, 19, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 19, 86, 86, 201, 19, 19, 19, 19, 19, 8, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [35, 36, 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, 43, 44])
total number of confs: 529
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497740 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(F)CCOCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 5, 7, 7, 6, 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: [72, 44, 13, 1, 1, 1, 1, 1, 1, 1, 72, 103, 103, 103, 103, 103, 149, 149, 149, 201, 201, 201, 201, 201, 201, 103, 44, 44, 1, 103, 103, 103, 103, 103, 149, 201, 201, 201, 201, 201, 201, 201, 201, 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, 44])
total number of confs: 654
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497740 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497740
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497740/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497740
Building REAL300025497741
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497741'
/scratch/stefan/7787277/working/building/REAL300025497741 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497741

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497741/0 /scratch/stefan/7787277/working/building/REAL300025497741 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 609)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/609
`/scratch/stefan/7787277/working/3D/609' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CNC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497741.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497741.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497741/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497741 none O=C(CCC1=CNC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [4, 4, 4, 6, 6, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 7, 15, 15, 15, 15, 15, 1, 6, 6, 6, 6, 7, 7, 7, 4, 1, 1, 1, 1, 1, 5, 5, 15, 1, 1] 19
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 52
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497741 none O=C(CCC1=CNC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [17, 17, 17, 19, 19, 19, 19, 19, 19, 15, 15, 15, 15, 15, 14, 13, 14, 9, 1, 1, 1, 1, 1, 1, 1, 15, 19, 19, 19, 19, 19, 19, 19, 17, 15, 15, 15, 15, 15, 13, 13, 1, 15, 15] 19
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])
total number of confs: 57
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497741 none O=C(CCC1=CNC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [4, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 7, 7, 7, 7, 7, 7, 7, 9, 12, 19, 19, 19, 19, 19, 7, 3, 3, 3, 3, 1, 1, 1, 4, 7, 7, 7, 7, 7, 9, 9, 19, 7, 7] 19
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 53
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497741 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497741/1 /scratch/stefan/7787277/working/building/REAL300025497741 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 610)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/610
`/scratch/stefan/7787277/working/3D/610' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CN=CN1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497741.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497741.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497741/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497741 none O=C(CCC1=CN=CN1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 19, 24, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 37, 117, 117, 117, 117, 117, 1, 19, 19, 24, 24, 26, 26, 26, 5, 1, 1, 1, 1, 1, 23, 23, 117, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 311
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497741 none O=C(CCC1=CN=CN1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [143, 143, 143, 198, 199, 201, 201, 201, 201, 117, 117, 117, 117, 117, 59, 29, 59, 12, 1, 1, 1, 1, 1, 1, 1, 117, 198, 198, 199, 199, 201, 201, 201, 143, 117, 117, 117, 117, 117, 29, 29, 1, 117, 117] 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])
total number of confs: 660
number of broken/clashed sets: 40
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497741 none O=C(CCC1=CN=CN1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [15, 5, 3, 1, 1, 1, 1, 1, 1, 15, 15, 26, 26, 26, 26, 26, 45, 45, 80, 118, 201, 201, 201, 201, 201, 26, 5, 5, 3, 3, 1, 1, 1, 15, 26, 26, 26, 26, 26, 80, 80, 201, 26, 26] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 522
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497741 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497741
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497741/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497741/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497741
Building REAL300025497742
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497742'
/scratch/stefan/7787277/working/building/REAL300025497742 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497742

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497742/0 /scratch/stefan/7787277/working/building/REAL300025497742 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 611)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/611
`/scratch/stefan/7787277/working/3D/611' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCN1C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497742.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497742.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497742/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497742 none C=CCN1C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 18, 10, 10, 10, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 15, 72, 72, 72, 72, 72, 1, 31, 31, 31, 18, 18, 10, 10, 10, 4, 1, 1, 1, 1, 1, 9, 9, 72, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 44, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 214
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497742 none C=CCN1C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 150, 150, 150, 150, 150, 98, 98, 98, 72, 72, 72, 72, 72, 53, 30, 53, 13, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 201, 150, 150, 150, 98, 72, 72, 72, 72, 72, 30, 30, 1, 72, 72] 201
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, 44, 45])
total number of confs: 700
number of broken/clashed sets: 83
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497742 none C=CCN1C=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 16, 16, 36, 58, 150, 150, 150, 150, 150, 10, 10, 10, 10, 4, 4, 1, 1, 1, 5, 10, 10, 10, 10, 10, 36, 36, 150, 10, 10] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 338
number of broken/clashed sets: 83
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497742 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497742
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497742/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497742
Building REAL300025497743
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497743'
/scratch/stefan/7787277/working/building/REAL300025497743 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497743

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497743/0 /scratch/stefan/7787277/working/building/REAL300025497743 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 612)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/612
`/scratch/stefan/7787277/working/3D/612' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+](CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1)

`REAL300025497743.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497743.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497743/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497743 none C[N@H+](CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [47, 47, 47, 36, 36, 36, 27, 27, 27, 27, 27, 21, 19, 21, 13, 1, 1, 1, 1, 1, 1, 1, 27, 47, 47, 47, 47, 47, 47, 47, 47, 47, 36, 27, 27, 27, 27, 27, 19, 19, 1, 27, 27, 47, 47, 47, 47, 47, 47, 47] 47
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 162
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497743 none C[N@H+](CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 3, 4, 7, 7, 7, 17, 17, 17, 17, 17, 20, 20, 33, 38, 47, 47, 47, 47, 47, 17, 1, 1, 1, 1, 3, 3, 3, 4, 4, 7, 17, 17, 17, 17, 17, 33, 33, 47, 17, 17, 1, 1, 1, 1, 1, 1, 1] 47
rigid atoms, others: [1, 43, 44, 45, 46, 47, 48, 49, 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])
total number of confs: 165
number of broken/clashed sets: 33
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497743 none C[N@H+](CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
47  conformations in input
total number of sets (complete confs): 47
using default count positions algorithm for smaller data
unique positions, atoms: [15, 13, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 14, 27, 27, 27, 27, 27, 1, 15, 17, 17, 17, 15, 15, 15, 13, 13, 5, 1, 1, 1, 1, 1, 9, 9, 27, 1, 1, 17, 17, 17, 17, 17, 17, 17] 47
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 126
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497743 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497743/1 /scratch/stefan/7787277/working/building/REAL300025497743 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 613)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/613
`/scratch/stefan/7787277/working/3D/613' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+](CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1)

`REAL300025497743.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497743.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497743/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497743 none C[N@@H+](CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [17, 17, 17, 12, 12, 12, 10, 10, 10, 10, 10, 10, 9, 10, 7, 1, 1, 1, 1, 1, 1, 1, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 10, 10, 10, 10, 10, 9, 9, 1, 10, 10, 17, 17, 17, 17, 17, 17, 17] 17
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 62
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497743 none C[N@@H+](CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [2, 1, 2, 2, 4, 5, 5, 5, 9, 9, 9, 9, 9, 11, 11, 16, 16, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 2, 2, 2, 4, 4, 5, 9, 9, 9, 9, 9, 16, 16, 17, 9, 9, 1, 1, 1, 1, 1, 1, 1] 17
rigid atoms, others: [1, 43, 44, 45, 46, 47, 48, 49, 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])
total number of confs: 68
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497743 none C[N@@H+](CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
17  conformations in input
total number of sets (complete confs): 17
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 5, 5, 10, 10, 10, 10, 10, 1, 8, 9, 9, 9, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 5, 5, 10, 1, 1, 9, 9, 9, 9, 9, 9, 9] 17
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 56
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497743 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497743
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497743/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497743/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497743
Building REAL300025497744
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497744'
/scratch/stefan/7787277/working/building/REAL300025497744 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497744

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497744/0 /scratch/stefan/7787277/working/building/REAL300025497744 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 614)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/614
`/scratch/stefan/7787277/working/3D/614' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NN3CCOC3=C2)C1)

`REAL300025497744.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497744.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497744/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497744 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NN3CCOC3=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 5, 5, 12, 1, 1, 5, 7, 7, 6, 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: [6, 1, 6, 35, 60, 159, 159, 159, 159, 159, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 1, 35, 35, 159, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 41, 10, 11, 12, 13, 14, 15, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40])
total number of confs: 325
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497744 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NN3CCOC3=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 5, 5, 12, 1, 1, 5, 7, 7, 6, 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: [31, 11, 31, 85, 120, 201, 201, 201, 201, 201, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 11, 85, 85, 201, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 11, 11] 201
rigid atoms, others: [36, 37, 38, 39, 40, 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, 41, 42])
total number of confs: 520
number of broken/clashed sets: 29
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497744 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NN3CCOC3=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 5, 5, 12, 1, 1, 5, 7, 7, 6, 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: [118, 46, 13, 1, 1, 1, 1, 1, 1, 1, 118, 159, 159, 159, 159, 159, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 159, 46, 46, 1, 159, 159, 159, 159, 159, 201, 201, 201, 201, 201, 201, 159, 159] 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: 596
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497744 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497744
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497744/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497744
Building REAL300025497745
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497745'
/scratch/stefan/7787277/working/building/REAL300025497745 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497745

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497745/0 /scratch/stefan/7787277/working/building/REAL300025497745 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 615)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/615
`/scratch/stefan/7787277/working/3D/615' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1CCOCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497745.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497745.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497745/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497745 none O=C(CN1CCOCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 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]
0  hydrogens 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, 24, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 22, 90, 90, 90, 90, 90, 1, 24, 24, 31, 31, 31, 31, 31, 31, 5, 1, 1, 1, 1, 1, 12, 12, 90, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 44, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 235
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497745 none O=C(CN1CCOCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 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]
0  hydrogens 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, 201, 90, 90, 90, 90, 90, 51, 29, 51, 12, 1, 1, 1, 1, 1, 1, 1, 90, 200, 200, 201, 201, 201, 201, 201, 201, 112, 90, 90, 90, 90, 90, 29, 29, 1, 90, 90] 201
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, 44, 45])
total number of confs: 737
number of broken/clashed sets: 45
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497745 none O=C(CN1CCOCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 5, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 31, 31, 31, 31, 31, 57, 57, 83, 122, 201, 201, 201, 201, 201, 31, 5, 5, 1, 1, 1, 1, 1, 1, 19, 31, 31, 31, 31, 31, 83, 83, 201, 31, 31] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 516
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497745 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497745
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497745/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497745
Building REAL300025497746
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497746'
/scratch/stefan/7787277/working/building/REAL300025497746 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497746

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497746/0 /scratch/stefan/7787277/working/building/REAL300025497746 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 616)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/616
`/scratch/stefan/7787277/working/3D/616' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025497746.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497746.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497746/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497746 none CCC1=CC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 32, 105, 105, 105, 105, 105, 1, 5, 14, 14, 14, 14, 14, 5, 5, 5, 5, 1, 1, 1, 1, 1, 18, 18, 105, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 242
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497746 none CCC1=CC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 127, 127, 127, 127, 127, 127, 127, 127, 105, 105, 105, 105, 105, 85, 39, 85, 13, 1, 1, 1, 1, 1, 1, 1, 105, 127, 201, 201, 201, 201, 201, 127, 127, 127, 127, 105, 105, 105, 105, 105, 39, 39, 1, 105, 105] 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])
total number of confs: 842
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497746 none CCC1=CC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 16, 16, 39, 61, 127, 127, 127, 127, 127, 5, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 39, 39, 127, 5, 5] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 9, 10, 7, 34, 35, 26] set([0, 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])
total number of confs: 304
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497746 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497746
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497746/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497746
Building REAL300025497747
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497747'
/scratch/stefan/7787277/working/building/REAL300025497747 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497747

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497747/0 /scratch/stefan/7787277/working/building/REAL300025497747 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 617)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/617
`/scratch/stefan/7787277/working/3D/617' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497747.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497747.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497747/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497747 none CC1=NN(C)C=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 45, 45, 45, 45, 45, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 11, 45, 45, 45, 45, 45, 1, 45, 45, 45, 45, 45, 45, 45, 23, 23, 5, 1, 1, 1, 1, 1, 7, 7, 45, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 185
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497747 none CC1=NN(C)C=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 157, 64, 64, 64, 45, 45, 45, 45, 45, 33, 26, 33, 13, 1, 1, 1, 1, 1, 1, 1, 45, 201, 201, 201, 201, 201, 201, 201, 157, 157, 64, 45, 45, 45, 45, 45, 26, 26, 1, 45, 45] 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])
total number of confs: 674
number of broken/clashed sets: 52
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497747 none CC1=NN(C)C=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 1, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total 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, 25, 25, 25, 45, 45, 45, 45, 45, 51, 51, 85, 120, 201, 201, 201, 201, 201, 45, 2, 2, 2, 2, 2, 2, 1, 8, 8, 25, 45, 45, 45, 45, 45, 85, 85, 201, 45, 45] 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: 549
number of broken/clashed sets: 52
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497747 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497747
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497747/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497747
Building REAL300025497748
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497748'
/scratch/stefan/7787277/working/building/REAL300025497748 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497748

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497748/0 /scratch/stefan/7787277/working/building/REAL300025497748 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 618)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/618
`/scratch/stefan/7787277/working/3D/618' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCC1)

`REAL300025497748.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497748.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497748/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497748 none CC(C)(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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: [196, 104, 196, 104, 104, 82, 82, 82, 82, 82, 54, 28, 54, 13, 1, 1, 1, 1, 1, 1, 1, 82, 196, 201, 201, 201, 201, 196, 196, 196, 196, 196, 196, 104, 82, 82, 82, 82, 82, 28, 28, 1, 82, 82, 201, 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: 795
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497748 none CC(C)(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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: [3, 1, 3, 3, 7, 7, 7, 16, 16, 16, 16, 16, 43, 43, 78, 123, 201, 201, 201, 201, 201, 16, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 7, 16, 16, 16, 16, 16, 78, 78, 201, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 44, 45, 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])
total number of confs: 501
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497748 none CC(C)(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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: [15, 5, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 28, 82, 82, 82, 82, 82, 1, 15, 16, 16, 16, 16, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 14, 14, 82, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16] 201
rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 43, 21, 38, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 203
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497748 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497748
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497748/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497748
Building REAL300025497749
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497749'
/scratch/stefan/7787277/working/building/REAL300025497749 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497749

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497749/0 /scratch/stefan/7787277/working/building/REAL300025497749 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 619)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/619
`/scratch/stefan/7787277/working/3D/619' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCCCC1)

`REAL300025497749.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497749.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497749/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497749 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 22, 55, 154, 154, 154, 154, 154, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 22, 22, 154, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 20, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 276
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497749 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 154, 154, 154, 154, 154, 125, 59, 125, 13, 1, 1, 1, 1, 1, 1, 1, 154, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 154, 154, 154, 154, 154, 59, 59, 1, 154, 154, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [38, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 614
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497749 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  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, 5, 5, 5, 5, 5, 13, 13, 41, 94, 201, 201, 201, 201, 201, 5, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 5, 5, 41, 41, 201, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 21, 22, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 418
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497749 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497749
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497749/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497749
Building REAL300025497750
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497750'
/scratch/stefan/7787277/working/building/REAL300025497750 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497750

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497750/0 /scratch/stefan/7787277/working/building/REAL300025497750 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 620)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/620
`/scratch/stefan/7787277/working/3D/620' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)C=N2)C1)

`REAL300025497750.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497750.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497750/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497750 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)C=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 21, 46, 133, 133, 133, 133, 133, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 1, 21, 21, 133, 1, 1, 1, 1, 1, 5, 8, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37])
total number of confs: 249
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497750 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)C=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 8, 24, 56, 97, 201, 201, 201, 201, 201, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 8, 56, 56, 201, 8, 8, 8, 8, 8, 3, 1, 1, 1, 8, 8] 201
rigid atoms, others: [35, 36, 37, 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, 38, 39])
total number of confs: 434
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497750 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(F)C=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 15, 1, 8, 5, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [97, 40, 13, 1, 1, 1, 1, 1, 1, 1, 97, 133, 133, 133, 133, 133, 201, 201, 201, 201, 201, 201, 201, 201, 201, 133, 40, 40, 1, 133, 133, 133, 133, 133, 201, 201, 201, 201, 133, 133] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 631
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497750 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497750
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497750/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497750
Building REAL300025497751
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497751'
/scratch/stefan/7787277/working/building/REAL300025497751 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497751

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497751/0 /scratch/stefan/7787277/working/building/REAL300025497751 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 621)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/621
`/scratch/stefan/7787277/working/3D/621' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COCC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497751.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497751.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497751/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497751 none O=C(COCC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 3, 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]
0  hydrogens need 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, 7, 13, 29, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 29, 29, 29, 29, 29, 1, 7, 7, 29, 29, 49, 49, 49, 49, 49, 49, 49, 49, 49, 3, 1, 1, 1, 1, 1, 4, 4, 29, 1, 1] 201
rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48])
total number of confs: 214
number of broken/clashed sets: 165
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497751 none O=C(COCC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 30, 30, 83, 112, 119, 201, 201, 201, 201, 29, 29, 29, 29, 29, 29, 24, 29, 13, 1, 1, 1, 1, 1, 1, 1, 29, 83, 83, 119, 119, 201, 201, 201, 201, 201, 201, 201, 201, 201, 30, 29, 29, 29, 29, 29, 24, 24, 1, 29, 29] 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, 50])
total number of confs: 669
number of broken/clashed sets: 165
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497751 none O=C(COCC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 3, 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]
0  hydrogens 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, 35, 14, 5, 1, 1, 1, 1, 1, 1, 48, 48, 49, 49, 49, 49, 49, 49, 49, 71, 106, 201, 201, 201, 201, 201, 49, 35, 35, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 49, 49, 49, 49, 49, 71, 71, 201, 49, 49] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 39, 36, 38, 37, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 513
number of broken/clashed sets: 165
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497751 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497751
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497751/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497751
Building REAL300025497752
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497752'
/scratch/stefan/7787277/working/building/REAL300025497752 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497752

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497752/0 /scratch/stefan/7787277/working/building/REAL300025497752 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 622)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/622
`/scratch/stefan/7787277/working/3D/622' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497752.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497752.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497752/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497752 none O=C(CCCC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 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, 7, 7, 7]
0  hydrogens need 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, 14, 16, 18, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 41, 41, 41, 41, 41, 1, 14, 14, 18, 18, 18, 18, 37, 37, 37, 37, 37, 37, 37, 37, 37, 3, 1, 1, 1, 1, 1, 5, 5, 41, 1, 1] 201
rigid atoms, others: [11, 47, 44, 10, 43, 12, 13, 14, 45, 16, 51, 52, 46, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 209
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497752 none O=C(CCCC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 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, 7, 7, 7]
0  hydrogens 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, 129, 114, 133, 201, 201, 201, 201, 41, 41, 41, 41, 41, 38, 27, 38, 12, 1, 1, 1, 1, 1, 1, 1, 41, 129, 129, 133, 133, 133, 133, 201, 201, 201, 201, 201, 201, 201, 201, 201, 42, 41, 41, 41, 41, 41, 27, 27, 1, 41, 41] 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: 907
number of broken/clashed sets: 53
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497752 none O=C(CCCC1CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 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, 7, 7, 7]
0  hydrogens 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, 8, 4, 4, 1, 1, 1, 1, 1, 1, 32, 32, 37, 37, 37, 37, 37, 39, 39, 85, 130, 201, 201, 201, 201, 201, 37, 8, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 37, 37, 37, 37, 37, 85, 85, 201, 37, 37] 201
rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 39, 40, 41, 36, 38, 37] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 560
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497752 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497752
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497752/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497752
Building REAL300025497753
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497753'
/scratch/stefan/7787277/working/building/REAL300025497753 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497753

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497753/0 /scratch/stefan/7787277/working/building/REAL300025497753 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 623)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/623
`/scratch/stefan/7787277/working/3D/623' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C1=O)

`REAL300025497753.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497753.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497753/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497753 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 11, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 34, 88, 88, 88, 88, 88, 1, 23, 23, 23, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 1, 19, 19, 88, 1, 1, 23, 23, 23] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44])
total number of confs: 210
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497753 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 11, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  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, 121, 121, 88, 88, 88, 88, 88, 72, 42, 72, 13, 1, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 201, 201, 201, 201, 201, 121, 88, 88, 88, 88, 88, 42, 42, 1, 88, 88, 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])
total number of confs: 527
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497753 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 1, 11, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 23, 23, 23, 23, 23, 54, 54, 97, 138, 201, 201, 201, 201, 201, 23, 1, 1, 1, 1, 2, 2, 2, 1, 8, 23, 23, 23, 23, 23, 97, 97, 201, 23, 23, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 564
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497753 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497753
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497753/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497753
Building REAL300025497754
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497754'
/scratch/stefan/7787277/working/building/REAL300025497754 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497754

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497754/0 /scratch/stefan/7787277/working/building/REAL300025497754 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 624)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/624
`/scratch/stefan/7787277/working/3D/624' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NSC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497754.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497754.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497754/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497754 none CC1=NSC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 14, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 19, 19, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 20, 66, 66, 66, 66, 66, 1, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 12, 12, 66, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 154
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497754 none CC1=NSC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 14, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 201, 89, 89, 89, 66, 66, 66, 66, 66, 55, 37, 55, 12, 1, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 201, 201, 201, 89, 66, 66, 66, 66, 66, 37, 37, 1, 66, 66] 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])
total number of confs: 501
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497754 none CC1=NSC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'S.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 14, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 19, 19, 19, 19, 19, 35, 35, 70, 103, 201, 201, 201, 201, 201, 19, 2, 2, 2, 2, 2, 2, 6, 19, 19, 19, 19, 19, 70, 70, 201, 19, 19] 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])
total number of confs: 528
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497754 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497754
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497754/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497754
Building REAL300025497755
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497755'
/scratch/stefan/7787277/working/building/REAL300025497755 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497755

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497755/0 /scratch/stefan/7787277/working/building/REAL300025497755 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 625)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/625
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2=CC=CC(C3CC3)=C2)C1)

`REAL300025497755.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497755.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497755/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025497755 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC(C3CC3)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 7, 7, 6, 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, 19, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 17, 17, 9, 1, 12, 12, 53, 1, 1, 1, 1, 1, 3, 9, 9, 9, 17, 17, 17, 17, 17, 9, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 47, 10, 11, 12, 13, 14, 15, 46, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 145
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.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: REAL300025497755 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC(C3CC3)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 7, 7, 6, 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: [43, 17, 43, 67, 107, 201, 201, 201, 201, 201, 17, 17, 17, 17, 9, 9, 3, 9, 3, 3, 3, 3, 1, 1, 1, 1, 3, 17, 67, 67, 201, 17, 17, 17, 17, 17, 9, 3, 3, 3, 1, 1, 1, 1, 1, 3, 17, 17] 201
rigid atoms, others: [40, 41, 42, 43, 44, 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, 45, 46, 47])
total number of confs: 478
number of broken/clashed sets: 78
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497755 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC(C3CC3)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 7, 7, 6, 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: [23, 9, 23, 35, 56, 127, 127, 127, 127, 127, 9, 9, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 9, 35, 35, 127, 9, 9, 9, 9, 9, 5, 1, 1, 1, 3, 3, 3, 3, 3, 1, 9, 9] 201
rigid atoms, others: [37, 38, 39, 45, 16, 18, 19, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 46, 47])
total number of confs: 276
number of broken/clashed sets: 78
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497755 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC(C3CC3)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 5, 5, 1, 5, 7, 7, 6, 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: [52, 37, 13, 1, 1, 1, 1, 1, 1, 1, 52, 53, 53, 53, 53, 53, 53, 53, 53, 127, 127, 127, 127, 127, 201, 201, 127, 53, 37, 37, 1, 53, 53, 53, 53, 53, 53, 127, 127, 127, 201, 201, 201, 201, 201, 127, 53, 53] 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: 585
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497755 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497755
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497755/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497755
Building REAL300025497756
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497756'
/scratch/stefan/7787277/working/building/REAL300025497756 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497756

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497756/0 /scratch/stefan/7787277/working/building/REAL300025497756 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 626)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/626
`/scratch/stefan/7787277/working/3D/626' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C)CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497756.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497756.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497756/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497756 none CC1CC(C)CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 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, 6, 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: [21, 21, 21, 21, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 27, 64, 64, 64, 64, 64, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 17, 17, 64, 1, 1, 21, 21] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 49, 50, 41, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 51, 52])
total number of confs: 186
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497756 none CC1CC(C)CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 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, 6, 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, 201, 77, 77, 77, 64, 64, 64, 64, 64, 57, 36, 57, 13, 1, 1, 1, 1, 1, 1, 1, 64, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 64, 64, 64, 64, 64, 36, 36, 1, 64, 64, 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: 622
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497756 none CC1CC(C)CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 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, 6, 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, 7, 7, 7, 21, 21, 21, 21, 21, 50, 50, 93, 135, 201, 201, 201, 201, 201, 21, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 1, 7, 21, 21, 21, 21, 21, 93, 93, 201, 21, 21, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 38, 7, 33, 37, 51, 52, 39, 26, 27, 28, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 558
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497756 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497756
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497756/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497756
Building REAL300025497757
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497757'
/scratch/stefan/7787277/working/building/REAL300025497757 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497757

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497757/0 /scratch/stefan/7787277/working/building/REAL300025497757 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 627)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/627
`/scratch/stefan/7787277/working/3D/627' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497757.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497757.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497757/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497757 none CC(=O)N1CCC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 12, 16, 12, 12, 12, 12, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 29, 85, 85, 85, 85, 85, 1, 16, 16, 16, 12, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 18, 18, 85, 1, 1] 201
rigid atoms, others: [47, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 206
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497757 none CC(=O)N1CCC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens need 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, 201, 152, 152, 152, 152, 139, 152, 139, 139, 85, 84, 84, 84, 84, 61, 26, 61, 12, 1, 1, 1, 1, 1, 1, 1, 84, 201, 201, 201, 152, 152, 152, 152, 152, 152, 139, 84, 84, 84, 84, 84, 26, 26, 1, 84, 84] 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, 46, 47])
total number of confs: 662
number of broken/clashed sets: 38
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497757 none CC(=O)N1CCC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 12, 12, 12, 12, 12, 24, 24, 54, 85, 152, 152, 152, 152, 152, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 12, 12, 12, 12, 12, 54, 54, 152, 12, 12] 201
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 33, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 367
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497757 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497757
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497757/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497757
Building REAL300025497758
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497758'
/scratch/stefan/7787277/working/building/REAL300025497758 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497758

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497758/0 /scratch/stefan/7787277/working/building/REAL300025497758 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 628)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/628
`/scratch/stefan/7787277/working/3D/628' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497758.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497758.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497758/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497758 none CC1(C)CCCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 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, 6, 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: [22, 22, 22, 22, 22, 22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 28, 62, 62, 62, 62, 62, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 1, 1, 1, 1, 1, 18, 18, 62, 1, 1, 22, 22] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 49, 50, 41, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 51, 52])
total number of confs: 188
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497758 none CC1(C)CCCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 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, 6, 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, 201, 75, 75, 75, 62, 62, 62, 62, 62, 57, 37, 57, 13, 1, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 75, 62, 62, 62, 62, 62, 37, 37, 1, 62, 62, 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: 623
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497758 none CC1(C)CCCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 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, 6, 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, 6, 6, 6, 22, 22, 22, 22, 22, 49, 49, 93, 136, 201, 201, 201, 201, 201, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 22, 22, 22, 93, 93, 201, 22, 22, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 51, 52] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 550
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497758 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497758
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497758/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497758
Building REAL300025497759
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497759'
/scratch/stefan/7787277/working/building/REAL300025497759 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497759

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497759/0 /scratch/stefan/7787277/working/building/REAL300025497759 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 629)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/629
`/scratch/stefan/7787277/working/3D/629' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1)

`REAL300025497759.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497759.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497759/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497759 none CC1(C)CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 6, 7, 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: [20, 20, 20, 20, 20, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 33, 81, 81, 81, 81, 81, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 4, 1, 1, 1, 1, 1, 18, 18, 81, 1, 1, 20, 20, 20, 20] 201
rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49, 50, 51, 52])
total number of confs: 208
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497759 none CC1(C)CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 6, 7, 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, 201, 100, 100, 100, 81, 81, 81, 81, 81, 70, 37, 70, 13, 1, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 100, 81, 81, 81, 81, 81, 37, 37, 1, 81, 81, 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: 630
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497759 none CC1(C)CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 6, 7, 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, 1, 9, 9, 9, 20, 20, 20, 20, 20, 49, 49, 105, 145, 201, 201, 201, 201, 201, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 105, 105, 201, 20, 20, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 49, 50, 51, 52] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 573
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497759 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497759
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497759/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497759
Building REAL300025497760
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497760'
/scratch/stefan/7787277/working/building/REAL300025497760 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497760

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497760/0 /scratch/stefan/7787277/working/building/REAL300025497760 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 630)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/630
`/scratch/stefan/7787277/working/3D/630' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(CF)C=C2)C1)

`REAL300025497760.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497760.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497760/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497760 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(CF)C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [5, 1, 5, 17, 36, 149, 149, 149, 149, 149, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 20, 9, 9, 1, 17, 17, 149, 1, 1, 1, 1, 1, 5, 9, 9, 20, 20, 9, 9, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 10, 11, 12, 13, 14, 15, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 300
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497760 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(CF)C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [20, 9, 20, 40, 69, 201, 201, 201, 201, 201, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 7, 1, 1, 9, 40, 40, 201, 9, 9, 9, 9, 9, 3, 1, 1, 7, 7, 1, 1, 9, 9] 201
rigid atoms, others: [36, 37, 40, 41, 16, 18, 19, 20, 21, 22, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 42, 43])
total number of confs: 399
number of broken/clashed sets: 38
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497760 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(CF)C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [124, 69, 13, 1, 1, 1, 1, 1, 1, 1, 124, 149, 149, 149, 149, 149, 155, 155, 155, 201, 201, 201, 201, 201, 201, 201, 149, 69, 69, 1, 149, 149, 149, 149, 149, 155, 201, 201, 201, 201, 201, 201, 149, 149] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 568
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497760 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497760
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497760/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497760
Building REAL300025497761
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497761'
/scratch/stefan/7787277/working/building/REAL300025497761 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497761

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497761/0 /scratch/stefan/7787277/working/building/REAL300025497761 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 631)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/631
`/scratch/stefan/7787277/working/3D/631' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(CC(C)C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497761.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497761.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497761/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497761 none CCCC(CC(C)C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens need rotated
201  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, 201, 201, 201, 201, 132, 132, 79, 79, 79, 79, 79, 57, 34, 57, 13, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 132, 79, 79, 79, 79, 79, 34, 34, 1, 79, 79] 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: 779
number of broken/clashed sets: 74
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497761 none CCCC(CC(C)C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens 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, 18, 5, 18, 24, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 16, 79, 79, 79, 79, 79, 1, 21, 21, 21, 21, 21, 21, 21, 18, 24, 24, 24, 24, 24, 24, 24, 24, 24, 5, 1, 1, 1, 1, 1, 9, 9, 79, 1, 1] 201
rigid atoms, others: [16, 15, 10, 11, 12, 13, 46, 45, 48, 49, 14, 54, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52])
total number of confs: 235
number of broken/clashed sets: 74
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497761 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497761
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497761/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497761
Building REAL300025497762
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497762'
/scratch/stefan/7787277/working/building/REAL300025497762 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497762

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497762/0 /scratch/stefan/7787277/working/building/REAL300025497762 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 632)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/632
`/scratch/stefan/7787277/working/3D/632' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497762.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497762.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497762/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497762 none CC1(C)CCCCC1C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 12, 12, 12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 48, 139, 139, 139, 139, 139, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 23, 23, 139, 1, 1] 201
rigid atoms, others: [11, 47, 44, 10, 43, 12, 13, 14, 45, 16, 51, 52, 46, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 279
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497762 none CC1(C)CCCCC1C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 172, 172, 172, 139, 139, 139, 139, 139, 108, 43, 108, 13, 1, 1, 1, 1, 1, 1, 1, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 172, 139, 139, 139, 139, 139, 43, 43, 1, 139, 139] 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: 637
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497762 none CC1(C)CCCCC1C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 30, 30, 81, 120, 201, 201, 201, 201, 201, 12, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 12, 81, 81, 201, 12, 12] 201
rigid atoms, others: [0, 1, 2, 3, 32, 33, 6, 7, 40, 41, 36, 34, 8, 35, 39, 4, 38, 5, 37, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 504
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497762 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497762
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497762/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497762
Building REAL300025497763
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497763'
/scratch/stefan/7787277/working/building/REAL300025497763 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497763

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497763/0 /scratch/stefan/7787277/working/building/REAL300025497763 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 633)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/633
`/scratch/stefan/7787277/working/3D/633' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(C)(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1)

`REAL300025497763.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497763.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497763/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497763 none CC1CCC(C)(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 6, 7, 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: [13, 13, 13, 13, 5, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 24, 63, 63, 63, 63, 63, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 15, 15, 63, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49, 50, 51, 52])
total number of confs: 165
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497763 none CC1CCC(C)(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 6, 7, 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, 77, 201, 77, 77, 63, 63, 63, 63, 63, 54, 40, 54, 11, 1, 1, 1, 1, 1, 1, 1, 63, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 63, 63, 63, 63, 63, 40, 40, 1, 63, 63, 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: 627
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497763 none CC1CCC(C)(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 6, 7, 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, 1, 3, 3, 3, 13, 13, 13, 13, 13, 36, 36, 69, 103, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 13, 13, 13, 13, 13, 69, 69, 201, 13, 13, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 49, 50, 51, 52, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 497
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497763 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497763
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497763/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497763
Building REAL300025497764
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497764'
/scratch/stefan/7787277/working/building/REAL300025497764 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497764

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497764/0 /scratch/stefan/7787277/working/building/REAL300025497764 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 634)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/634
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)[C@H]2[C@H]3[C@@H]2[C@@H]2CC[C@H]3C2)C1)

`REAL300025497764.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497764.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497764/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497764 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2[C@H]3[C@@H]2[C@@H]2CC[C@H]3C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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, 12, 18, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 4, 4, 4, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 12, 12, 52, 1, 1, 1, 1, 1, 4, 19, 19, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [1, 35, 36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 48, 47, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 145
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497764 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2[C@H]3[C@@H]2[C@@H]2CC[C@H]3C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [39, 19, 39, 76, 108, 201, 201, 201, 201, 201, 19, 19, 19, 19, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 76, 76, 201, 19, 19, 19, 19, 19, 11, 1, 1, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 47, 48])
total number of confs: 506
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497764 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2[C@H]3[C@@H]2[C@@H]2CC[C@H]3C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 7, 5, 7, 5, 7, 5, 5, 5, 7, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [38, 25, 11, 1, 1, 1, 1, 1, 1, 1, 38, 52, 52, 52, 52, 52, 77, 77, 77, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 52, 25, 25, 1, 52, 52, 52, 52, 52, 77, 201, 201, 201, 201, 201, 201, 52, 52] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 623
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497764 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497764
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497764/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497764
Building REAL300025497765
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497765'
/scratch/stefan/7787277/working/building/REAL300025497765 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497765

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497765/0 /scratch/stefan/7787277/working/building/REAL300025497765 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 635)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/635
`/scratch/stefan/7787277/working/3D/635' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1CCCO1)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497765.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497765.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497765/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497765 none CC(CC1CCCO1)C(=O)NC1C=CCN(C(=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.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 5, 14, 20, 25, 25, 25, 25, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 19, 78, 78, 78, 78, 78, 1, 14, 14, 14, 14, 20, 20, 25, 25, 25, 25, 25, 25, 25, 5, 1, 1, 1, 1, 1, 11, 11, 78, 1, 1] 201
rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48])
total number of confs: 227
number of broken/clashed sets: 68
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497765 none CC(CC1CCCO1)C(=O)NC1C=CCN(C(=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.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 115, 185, 186, 201, 201, 201, 201, 115, 115, 78, 78, 78, 78, 78, 60, 29, 60, 13, 1, 1, 1, 1, 1, 1, 1, 78, 185, 185, 185, 185, 186, 186, 201, 201, 201, 201, 201, 201, 201, 115, 78, 78, 78, 78, 78, 29, 29, 1, 78, 78] 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, 50])
total number of confs: 754
number of broken/clashed sets: 68
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497765 none CC(CC1CCCO1)C(=O)NC1C=CCN(C(=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.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 8, 15, 15, 15, 25, 25, 25, 25, 25, 35, 35, 78, 122, 201, 201, 201, 201, 201, 25, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 15, 25, 25, 25, 25, 25, 78, 78, 201, 25, 25] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 39, 34, 35, 36, 38, 37] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 544
number of broken/clashed sets: 68
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497765 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497765
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497765/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497765
Building REAL300025497766
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497766'
/scratch/stefan/7787277/working/building/REAL300025497766 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497766

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497766/0 /scratch/stefan/7787277/working/building/REAL300025497766 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 636)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/636
`/scratch/stefan/7787277/working/3D/636' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1)

`REAL300025497766.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497766.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497766/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497766 none CC(C)C1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 26, 96, 96, 96, 96, 96, 1, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 14, 14, 96, 1, 1, 20, 20] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46])
total number of confs: 189
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497766 none CC(C)C1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 132, 132, 132, 96, 96, 96, 96, 96, 59, 30, 59, 13, 1, 1, 1, 1, 1, 1, 1, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 132, 96, 96, 96, 96, 96, 30, 30, 1, 96, 96, 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])
total number of confs: 512
number of broken/clashed sets: 39
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497766 none CC(C)C1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7]
0  hydrogens need rotated
201  conformations in input
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, 20, 20, 20, 20, 20, 52, 52, 93, 126, 201, 201, 201, 201, 201, 20, 1, 1, 1, 2, 2, 2, 1, 2, 2, 2, 7, 20, 20, 20, 20, 20, 93, 93, 201, 20, 20, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 46, 24, 25, 26, 30] set([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])
total number of confs: 535
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497766 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497766
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497766/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497766
Building REAL300025497767
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497767'
/scratch/stefan/7787277/working/building/REAL300025497767 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497767

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497767/0 /scratch/stefan/7787277/working/building/REAL300025497767 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 637)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/637
`/scratch/stefan/7787277/working/3D/637' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497767.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497767.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497767/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497767 none CCOCCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  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, 167, 138, 128, 29, 29, 29, 28, 28, 28, 28, 28, 28, 22, 28, 13, 1, 1, 1, 1, 1, 1, 1, 28, 201, 201, 201, 201, 201, 183, 190, 167, 167, 167, 167, 167, 167, 128, 128, 29, 28, 28, 28, 28, 28, 22, 22, 1, 28, 28] 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: 1185
number of broken/clashed sets: 167
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497767 none CCOCCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens 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, 43, 16, 20, 16, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 7, 28, 28, 28, 28, 28, 1, 51, 51, 51, 51, 51, 41, 40, 20, 20, 20, 20, 20, 20, 11, 11, 3, 1, 1, 1, 1, 1, 5, 5, 28, 1, 1] 201
rigid atoms, others: [11, 47, 44, 10, 43, 12, 13, 14, 45, 16, 51, 52, 46, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 286
number of broken/clashed sets: 167
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497767 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497767
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497767/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497767
Building REAL300025497768
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497768'
/scratch/stefan/7787277/working/building/REAL300025497768 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497768

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497768/0 /scratch/stefan/7787277/working/building/REAL300025497768 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 638)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/638
`/scratch/stefan/7787277/working/3D/638' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)CCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497768.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497768.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497768/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497768 none CNC(=O)CCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [72, 72, 72, 72, 62, 60, 57, 27, 27, 27, 26, 26, 26, 26, 26, 26, 22, 26, 12, 1, 1, 1, 1, 1, 1, 1, 26, 72, 72, 72, 72, 72, 72, 62, 62, 62, 62, 57, 57, 27, 26, 26, 26, 26, 26, 22, 22, 1, 26, 26] 72
rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49])
total number of confs: 309
number of broken/clashed sets: 68
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497768 none CNC(=O)CCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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, 7]
0  hydrogens need rotated
72  conformations in input
total number of sets (complete confs): 72
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 18, 27, 13, 12, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 26, 26, 26, 26, 26, 1, 27, 27, 27, 27, 18, 18, 13, 13, 13, 13, 11, 11, 3, 1, 1, 1, 1, 1, 5, 5, 26, 1, 1] 72
rigid atoms, others: [48, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 153
number of broken/clashed sets: 68
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497768 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497768
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497768/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497768
Building REAL300025497769
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497769'
/scratch/stefan/7787277/working/building/REAL300025497769 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497769

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497769/0 /scratch/stefan/7787277/working/building/REAL300025497769 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 639)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/639
`/scratch/stefan/7787277/working/3D/639' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)C1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497769.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497769.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497769/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497769 none CC(C)(C)C1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 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, 6, 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: [23, 23, 23, 23, 23, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 25, 71, 71, 71, 71, 71, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 1, 14, 14, 71, 1, 1, 23, 23] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 49, 50, 41, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48, 51, 52])
total number of confs: 188
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497769 none CC(C)(C)C1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 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, 6, 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, 201, 100, 100, 100, 71, 71, 71, 71, 71, 64, 37, 64, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 100, 71, 71, 71, 71, 71, 37, 37, 1, 71, 71, 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: 660
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497769 none CC(C)(C)C1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 8, 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, 6, 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: [2, 1, 2, 2, 1, 1, 1, 1, 8, 8, 8, 23, 23, 23, 23, 23, 52, 52, 99, 142, 201, 201, 201, 201, 201, 23, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 8, 23, 23, 23, 23, 23, 99, 99, 201, 23, 23, 1, 1] 201
rigid atoms, others: [1, 4, 5, 6, 7, 39, 51, 52, 36, 26, 38, 37] set([0, 2, 3, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 573
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497769 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497769
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497769/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497769
Building REAL300025497770
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497770'
/scratch/stefan/7787277/working/building/REAL300025497770 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497770

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497770/0 /scratch/stefan/7787277/working/building/REAL300025497770 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 640)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/640
`/scratch/stefan/7787277/working/3D/640' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1C)

`REAL300025497770.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497770.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497770/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497770 none CC1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 37, 83, 83, 83, 83, 83, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 21, 21, 83, 1, 1, 13, 13, 13, 13, 13, 13] 201
rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 45, 40, 41, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47, 48, 49, 50, 51, 52])
total number of confs: 204
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497770 none CC1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 124, 124, 124, 83, 83, 83, 83, 83, 71, 40, 71, 13, 1, 1, 1, 1, 1, 1, 1, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 83, 83, 83, 83, 83, 40, 40, 1, 83, 83, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 661
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497770 none CC1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 39, 39, 92, 129, 201, 201, 201, 201, 201, 13, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 13, 92, 92, 201, 13, 13, 1, 1, 1, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 47, 48, 49, 35, 24, 25, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 50, 51, 52])
total number of confs: 542
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497770 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497770
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497770/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497770
Building REAL300025497771
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497771'
/scratch/stefan/7787277/working/building/REAL300025497771 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497771

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497771/0 /scratch/stefan/7787277/working/building/REAL300025497771 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 641)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/641
`/scratch/stefan/7787277/working/3D/641' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497771.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497771.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497771/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497771 none COC1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 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: [15, 15, 15, 15, 15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 39, 138, 138, 138, 138, 138, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 20, 20, 138, 1, 1] 201
rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48])
total number of confs: 272
number of broken/clashed sets: 51
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497771 none COC1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 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, 187, 187, 187, 138, 138, 138, 138, 138, 78, 30, 78, 13, 1, 1, 1, 1, 1, 1, 1, 138, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 187, 138, 138, 138, 138, 138, 30, 30, 1, 138, 138] 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, 50])
total number of confs: 578
number of broken/clashed sets: 51
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497771 none COC1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 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: [2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 15, 15, 15, 45, 45, 87, 123, 201, 201, 201, 201, 201, 15, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 15, 87, 87, 201, 15, 15] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 39, 34, 35, 36, 33, 38, 37, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 518
number of broken/clashed sets: 51
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497771 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497771
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497771/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497771
Building REAL300025497772
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497772'
/scratch/stefan/7787277/working/building/REAL300025497772 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497772

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497772/0 /scratch/stefan/7787277/working/building/REAL300025497772 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 642)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/642
`/scratch/stefan/7787277/working/3D/642' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497772.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497772.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497772/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497772 none C=CCCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
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, 128, 96, 39, 39, 39, 35, 35, 35, 35, 35, 35, 26, 35, 13, 1, 1, 1, 1, 1, 1, 1, 35, 201, 201, 201, 201, 201, 133, 133, 96, 96, 39, 35, 35, 35, 35, 35, 26, 26, 1, 35, 35] 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])
total number of confs: 807
number of broken/clashed sets: 163
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497772 none C=CCCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 37, 24, 14, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 35, 35, 35, 35, 35, 1, 45, 45, 45, 37, 37, 24, 24, 7, 7, 3, 1, 1, 1, 1, 1, 4, 4, 35, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 231
number of broken/clashed sets: 163
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497772 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497772
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497772/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497772
Building REAL300025497773
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497773'
/scratch/stefan/7787277/working/building/REAL300025497773 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497773

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497773/0 /scratch/stefan/7787277/working/building/REAL300025497773 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 643)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/643
`/scratch/stefan/7787277/working/3D/643' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCOC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497773.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497773.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497773/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497773 none C=CCOC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 178, 171, 130, 171, 130, 130, 82, 82, 82, 82, 82, 59, 31, 58, 13, 1, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 201, 201, 171, 171, 171, 171, 130, 82, 82, 82, 82, 82, 31, 31, 1, 82, 82] 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])
total number of confs: 789
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497773 none C=CCOC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 16, 6, 5, 4, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 16, 82, 82, 82, 82, 82, 1, 28, 28, 28, 16, 16, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 8, 8, 82, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 217
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497773 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497773
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497773/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497773
Building REAL300025497774
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497774'
/scratch/stefan/7787277/working/building/REAL300025497774 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497774

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497774/0 /scratch/stefan/7787277/working/building/REAL300025497774 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 644)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/644
`/scratch/stefan/7787277/working/3D/644' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CCOC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497774.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497774.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497774/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497774 none CC(C)CCOC(C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens need rotated
201  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, 153, 140, 92, 140, 92, 92, 50, 50, 50, 50, 50, 43, 28, 42, 13, 1, 1, 1, 1, 1, 1, 1, 50, 201, 201, 201, 201, 201, 201, 201, 201, 201, 169, 169, 140, 140, 140, 140, 92, 50, 50, 50, 50, 50, 28, 28, 1, 50, 50] 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: 862
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: REAL300025497774 none CC(C)CCOC(C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens 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, 28, 15, 10, 4, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 13, 50, 50, 50, 50, 50, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 28, 28, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 8, 8, 50, 1, 1] 201
rigid atoms, others: [11, 47, 44, 10, 43, 12, 13, 14, 45, 16, 51, 52, 46, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 273
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497774 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497774
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497774/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497774
Building REAL300025497775
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497775'
/scratch/stefan/7787277/working/building/REAL300025497775 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497775

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497775/0 /scratch/stefan/7787277/working/building/REAL300025497775 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 645)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/645
`/scratch/stefan/7787277/working/3D/645' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1)

`REAL300025497775.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497775.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497775/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497775 none CCC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 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, 7, 7, 7, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 20, 34, 99, 99, 99, 99, 99, 1, 7, 20, 20, 20, 20, 20, 7, 5, 1, 1, 1, 1, 1, 20, 20, 99, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 261
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497775 none CCC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 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, 122, 122, 122, 122, 122, 122, 122, 99, 99, 99, 99, 99, 78, 39, 78, 13, 1, 1, 1, 1, 1, 1, 1, 99, 122, 201, 201, 201, 201, 201, 122, 122, 99, 99, 99, 99, 99, 39, 39, 1, 99, 99] 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])
total number of confs: 861
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497775 none CCC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 16, 16, 39, 58, 122, 122, 122, 122, 122, 7, 1, 5, 5, 5, 5, 5, 1, 4, 7, 7, 7, 7, 7, 39, 39, 122, 7, 7] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 304
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497775 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497775
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497775/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497775
Building REAL300025497776
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497776'
/scratch/stefan/7787277/working/building/REAL300025497776 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497776

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497776/0 /scratch/stefan/7787277/working/building/REAL300025497776 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 646)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/646
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2=CC=CC3=C2CCC3)C1)

`REAL300025497776.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497776.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497776/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497776 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC3=C2CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 6, 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, 13, 20, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 14, 19, 19, 19, 19, 19, 1, 13, 13, 74, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 47, 10, 11, 12, 13, 14, 15, 46, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 177
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497776 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC3=C2CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 6, 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: [45, 19, 45, 82, 114, 201, 201, 201, 201, 201, 19, 19, 19, 19, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 82, 82, 201, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47])
total number of confs: 521
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497776 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC3=C2CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 6, 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, 36, 13, 1, 1, 1, 1, 1, 1, 1, 56, 74, 74, 74, 74, 74, 109, 109, 109, 201, 201, 201, 201, 201, 201, 201, 201, 74, 36, 36, 1, 74, 74, 74, 74, 74, 109, 201, 201, 201, 201, 201, 201, 201, 201, 201, 74, 74] 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: 489
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497776 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497776
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497776/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497776
Building REAL300025497777
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497777'
/scratch/stefan/7787277/working/building/REAL300025497777 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497777

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497777/0 /scratch/stefan/7787277/working/building/REAL300025497777 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 647)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/647
`/scratch/stefan/7787277/working/3D/647' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497777.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497777.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497777/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497777 none CC1=CN=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 7, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 23, 88, 88, 88, 88, 88, 1, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 12, 12, 88, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 196
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497777 none CC1=CN=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  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, 201, 201, 113, 113, 113, 88, 88, 88, 88, 88, 74, 39, 74, 13, 1, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 201, 201, 201, 113, 88, 88, 88, 88, 88, 39, 39, 1, 88, 88] 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])
total number of confs: 596
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497777 none CC1=CN=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 21, 21, 21, 21, 21, 52, 52, 88, 121, 201, 201, 201, 201, 201, 21, 2, 2, 2, 1, 1, 1, 9, 21, 21, 21, 21, 21, 88, 88, 201, 21, 21] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 537
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497777 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497777
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497777/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497777
Building REAL300025497778
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497778'
/scratch/stefan/7787277/working/building/REAL300025497778 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497778

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497778/0 /scratch/stefan/7787277/working/building/REAL300025497778 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 648)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/648
`/scratch/stefan/7787277/working/3D/648' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3C=CNC3=C2)C1)

`REAL300025497778.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497778.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497778/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497778 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3C=CNC3=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 1, 5, 7, 7, 6, 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 14, 27, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 1, 14, 14, 91, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 185
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497778 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3C=CNC3=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 1, 5, 7, 7, 6, 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 15, 38, 72, 110, 201, 201, 201, 201, 201, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 72, 72, 201, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 15, 15] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 500
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497778 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3C=CNC3=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 8, 1, 1, 5, 7, 7, 6, 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, 3, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 50, 13, 1, 1, 1, 1, 1, 1, 1, 74, 91, 91, 91, 91, 91, 108, 108, 108, 201, 201, 201, 201, 201, 201, 201, 201, 91, 50, 50, 1, 91, 91, 91, 91, 91, 108, 201, 201, 201, 201, 201, 91, 91] 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: 486
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497778 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497778
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497778/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497778
Building REAL300025497779
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497779'
/scratch/stefan/7787277/working/building/REAL300025497779 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497779

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497779/0 /scratch/stefan/7787277/working/building/REAL300025497779 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 649)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/649
`/scratch/stefan/7787277/working/3D/649' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC2(F)F)C1)

`REAL300025497779.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497779.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497779/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497779 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC2(F)F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 7, 7, 6, 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]
0  hydrogens 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, 24, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 1, 4, 4, 4, 26, 26, 26, 26, 26, 1, 14, 14, 83, 1, 1, 1, 1, 1, 4, 26, 26, 26, 26, 26, 1, 1] 201
rigid atoms, others: [32, 1, 39, 40, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38])
total number of confs: 197
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497779 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC2(F)F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 7, 7, 6, 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]
0  hydrogens 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, 26, 51, 87, 122, 201, 201, 201, 201, 201, 26, 26, 26, 26, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 26, 87, 87, 201, 26, 26, 26, 26, 26, 12, 1, 1, 1, 1, 1, 26, 26] 201
rigid atoms, others: [34, 35, 36, 37, 38, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40])
total number of confs: 529
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497779 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC2(F)F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 15, 15, 5, 7, 7, 6, 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]
0  hydrogens 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, 35, 13, 1, 1, 1, 1, 1, 1, 1, 62, 83, 83, 83, 83, 83, 121, 121, 121, 201, 201, 201, 201, 201, 83, 35, 35, 1, 83, 83, 83, 83, 83, 121, 201, 201, 201, 201, 201, 83, 83] 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: 647
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497779 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497779
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497779/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497779
Building REAL300025497780
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497780'
/scratch/stefan/7787277/working/building/REAL300025497780 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497780

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497780/0 /scratch/stefan/7787277/working/building/REAL300025497780 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 650)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/650
`/scratch/stefan/7787277/working/3D/650' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NSC=C2)C1)

`REAL300025497780.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497780.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497780/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497780 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NSC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 14, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 47, 140, 140, 140, 140, 140, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 1, 21, 21, 140, 1, 1, 1, 1, 1, 5, 8, 8, 1, 1] 201
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34])
total number of confs: 258
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497780 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NSC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 14, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 25, 59, 100, 201, 201, 201, 201, 201, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 59, 59, 201, 8, 8, 8, 8, 8, 3, 1, 1, 8, 8] 201
rigid atoms, others: [33, 34, 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, 35, 36])
total number of confs: 449
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497780 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NSC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'S.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 14, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 44, 13, 1, 1, 1, 1, 1, 1, 1, 106, 140, 140, 140, 140, 140, 201, 201, 201, 201, 201, 201, 201, 140, 44, 44, 1, 140, 140, 140, 140, 140, 201, 201, 201, 140, 140] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 630
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497780 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497780
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497780/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497780
Building REAL300025497781
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497781'
/scratch/stefan/7787277/working/building/REAL300025497781 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497781

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497781/0 /scratch/stefan/7787277/working/building/REAL300025497781 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 651)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/651
`/scratch/stefan/7787277/working/3D/651' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497781.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497781.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497781/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497781 none CCOC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 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]
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: [22, 13, 9, 9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 53, 146, 146, 146, 146, 146, 1, 9, 22, 22, 22, 22, 22, 9, 5, 1, 1, 1, 1, 1, 29, 29, 146, 1, 1, 9] 192
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44])
total number of confs: 347
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497781 none CCOC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 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]
0  hydrogens need rotated
192  conformations in input
total number of sets (complete confs): 192
using faster count positions algorithm for large data
unique positions, atoms: [192, 190, 188, 188, 188, 188, 185, 185, 185, 146, 146, 146, 146, 146, 113, 46, 113, 13, 1, 1, 1, 1, 1, 1, 1, 146, 188, 192, 192, 192, 192, 192, 188, 185, 146, 146, 146, 146, 146, 46, 46, 1, 146, 146, 188] 192
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: 585
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497781 none CCOC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 7, 3, 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]
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: [9, 4, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 29, 29, 65, 101, 188, 188, 188, 188, 188, 9, 1, 9, 9, 9, 9, 9, 1, 4, 9, 9, 9, 9, 9, 65, 65, 188, 9, 9, 1] 192
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 44, 26] set([0, 1, 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])
total number of confs: 465
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497781 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497781
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497781/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497781
Building REAL300025497782
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497782'
/scratch/stefan/7787277/working/building/REAL300025497782 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497782

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497782/0 /scratch/stefan/7787277/working/building/REAL300025497782 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 652)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/652
`/scratch/stefan/7787277/working/3D/652' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=CC=CN3C=N2)C1)

`REAL300025497782.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497782.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497782/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497782 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=CC=CN3C=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 7, 7, 6, 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, 29, 55, 138, 138, 138, 138, 138, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 13, 13, 13, 13, 13, 12, 1, 29, 29, 138, 1, 1, 1, 1, 1, 6, 13, 13, 13, 13, 13, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 290
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497782 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=CC=CN3C=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 7, 7, 6, 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, 13, 35, 88, 130, 201, 201, 201, 201, 201, 13, 13, 13, 13, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 88, 88, 201, 13, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 13, 13] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 539
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497782 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=CC=CN3C=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 8, 5, 7, 7, 6, 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: [106, 40, 13, 1, 1, 1, 1, 1, 1, 1, 106, 138, 138, 138, 138, 138, 196, 196, 196, 201, 201, 201, 201, 201, 201, 201, 201, 138, 40, 40, 1, 138, 138, 138, 138, 138, 196, 201, 201, 201, 201, 201, 138, 138] 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: 613
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497782 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497782
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497782/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497782
Building REAL300025497783
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497783'
/scratch/stefan/7787277/working/building/REAL300025497783 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497783

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497783/0 /scratch/stefan/7787277/working/building/REAL300025497783 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 653)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/653
`/scratch/stefan/7787277/working/3D/653' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)S1)

`REAL300025497783.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497783.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497783/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497783 none CC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 14, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 55, 143, 143, 143, 143, 143, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 32, 32, 143, 1, 1, 11, 11, 11] 201
rigid atoms, others: [32, 33, 34, 38, 6, 7, 8, 9, 10, 11, 12, 22, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42])
total number of confs: 299
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497783 none CC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 14, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  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, 143, 143, 143, 143, 143, 103, 41, 103, 13, 1, 1, 1, 1, 1, 1, 1, 143, 201, 201, 201, 201, 201, 201, 200, 143, 143, 143, 143, 143, 41, 41, 1, 143, 143, 201, 201, 201] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 604
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497783 none CC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 14, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 36, 36, 90, 128, 201, 201, 201, 201, 201, 11, 1, 1, 1, 2, 2, 2, 3, 11, 11, 11, 11, 11, 90, 90, 201, 11, 11, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 548
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497783 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497783
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497783/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497783
Building REAL300025497784
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497784'
/scratch/stefan/7787277/working/building/REAL300025497784 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497784

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497784/0 /scratch/stefan/7787277/working/building/REAL300025497784 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 654)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/654
`/scratch/stefan/7787277/working/3D/654' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1)

`REAL300025497784.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497784.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497784/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497784 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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, 122, 122, 122, 96, 96, 96, 96, 96, 62, 30, 62, 13, 1, 1, 1, 1, 1, 1, 1, 96, 201, 201, 201, 201, 201, 201, 201, 201, 122, 96, 96, 96, 96, 96, 30, 30, 1, 96, 96, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 758
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497784 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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: [3, 1, 3, 12, 12, 12, 27, 27, 27, 27, 27, 53, 53, 92, 133, 201, 201, 201, 201, 201, 27, 1, 1, 1, 1, 3, 3, 3, 3, 12, 27, 27, 27, 27, 27, 92, 92, 201, 27, 27, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 40, 41, 42, 43, 44, 45, 46, 21, 22, 23, 24] set([0, 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])
total number of confs: 542
number of broken/clashed sets: 50
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497784 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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: [22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 26, 96, 96, 96, 96, 96, 1, 22, 27, 27, 27, 22, 22, 22, 22, 5, 1, 1, 1, 1, 1, 13, 13, 96, 1, 1, 27, 27, 27, 27, 27, 27, 27] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 39, 20, 38, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 251
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497784 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497784
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497784/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497784
Building REAL300025497785
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497785'
/scratch/stefan/7787277/working/building/REAL300025497785 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497785

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497785/0 /scratch/stefan/7787277/working/building/REAL300025497785 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 655)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/655
`/scratch/stefan/7787277/working/3D/655' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1C=CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497785.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497785.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497785/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497785 none O=C(CC1C=CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 24, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 14, 59, 59, 59, 59, 59, 1, 24, 24, 40, 40, 40, 40, 40, 40, 40, 40, 40, 5, 1, 1, 1, 1, 1, 8, 8, 59, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 233
number of broken/clashed sets: 62
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497785 none O=C(CC1C=CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 201, 201, 201, 59, 59, 59, 59, 59, 47, 29, 47, 13, 1, 1, 1, 1, 1, 1, 1, 59, 195, 195, 201, 201, 201, 201, 201, 201, 201, 201, 201, 95, 59, 59, 59, 59, 59, 29, 29, 1, 59, 59] 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])
total number of confs: 784
number of broken/clashed sets: 62
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497785 none O=C(CC1C=CCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 19, 19, 40, 40, 40, 40, 40, 51, 51, 90, 134, 201, 201, 201, 201, 201, 40, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 40, 40, 40, 40, 40, 90, 90, 201, 40, 40] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 561
number of broken/clashed sets: 62
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497785 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497785
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497785/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497785
Building REAL300025497786
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497786'
/scratch/stefan/7787277/working/building/REAL300025497786 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497786

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497786/0 /scratch/stefan/7787277/working/building/REAL300025497786 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 656)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/656
`/scratch/stefan/7787277/working/3D/656' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CC=C(F)C=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497786.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497786.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497786/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497786 none O=C(CC1=CC=C(F)C=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens 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, 18, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 23, 89, 89, 89, 89, 89, 1, 18, 18, 20, 20, 20, 4, 1, 1, 1, 1, 1, 14, 14, 89, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 41, 10, 11, 12, 13, 14, 15, 16, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 209
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497786 none O=C(CC1=CC=C(F)C=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens 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, 201, 201, 201, 201, 201, 201, 201, 89, 89, 89, 89, 89, 52, 28, 52, 13, 1, 1, 1, 1, 1, 1, 1, 89, 201, 201, 201, 201, 201, 112, 89, 89, 89, 89, 89, 28, 28, 1, 89, 89] 201
rigid atoms, others: [40, 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, 41, 42])
total number of confs: 747
number of broken/clashed sets: 40
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497786 none O=C(CC1=CC=C(F)C=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 15, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 5, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 20, 20, 20, 20, 20, 50, 50, 82, 118, 201, 201, 201, 201, 201, 20, 5, 5, 1, 1, 1, 11, 20, 20, 20, 20, 20, 82, 82, 201, 20, 20] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 523
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497786 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497786
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497786/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497786
Building REAL300025497787
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497787'
/scratch/stefan/7787277/working/building/REAL300025497787 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497787

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497787/0 /scratch/stefan/7787277/working/building/REAL300025497787 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 657)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/657
`/scratch/stefan/7787277/working/3D/657' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1)

`REAL300025497787.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497787.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497787/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497787 none CCOCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 31, 16, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 21, 78, 78, 78, 78, 78, 1, 10, 10, 34, 34, 34, 34, 34, 16, 16, 4, 1, 1, 1, 1, 1, 12, 12, 78, 1, 1, 10, 10, 10, 10] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47])
total number of confs: 225
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497787 none CCOCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
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, 178, 114, 114, 114, 78, 78, 78, 78, 78, 61, 29, 61, 13, 1, 1, 1, 1, 1, 1, 1, 78, 178, 178, 201, 201, 201, 201, 201, 197, 197, 114, 78, 78, 78, 78, 78, 29, 29, 1, 78, 78, 178, 178, 178, 178] 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: 662
number of broken/clashed sets: 59
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497787 none CCOCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 16, 6, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 15, 15, 43, 74, 178, 178, 178, 178, 178, 10, 1, 1, 19, 19, 19, 19, 19, 6, 6, 6, 10, 10, 10, 10, 10, 43, 43, 178, 10, 10, 1, 1, 1, 1] 201
rigid atoms, others: [3, 4, 5, 44, 45, 46, 47, 24, 25] set([0, 1, 2, 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: 420
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497787 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497787
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497787/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497787
Building REAL300025497788
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497788'
/scratch/stefan/7787277/working/building/REAL300025497788 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497788

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497788/0 /scratch/stefan/7787277/working/building/REAL300025497788 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 658)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/658
`/scratch/stefan/7787277/working/3D/658' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CC(F)(F)C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497788.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497788.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497788/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497788 none O=C(CC1CC(F)(F)C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 15, 15, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 25, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 10, 49, 49, 49, 49, 49, 1, 25, 25, 51, 51, 51, 51, 51, 5, 1, 1, 1, 1, 1, 5, 5, 49, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 238
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497788 none O=C(CC1CC(F)(F)C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 15, 15, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [89, 89, 89, 165, 201, 201, 201, 201, 201, 49, 49, 49, 49, 49, 43, 29, 43, 13, 1, 1, 1, 1, 1, 1, 1, 49, 165, 165, 201, 201, 201, 201, 201, 89, 49, 49, 49, 49, 49, 29, 29, 1, 49, 49] 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])
total number of confs: 822
number of broken/clashed sets: 67
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497788 none O=C(CC1CC(F)(F)C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 15, 15, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 51, 51, 51, 51, 51, 59, 59, 103, 144, 201, 201, 201, 201, 201, 51, 5, 5, 1, 1, 1, 1, 1, 24, 51, 51, 51, 51, 51, 103, 103, 201, 51, 51] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 579
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497788 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497788
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497788/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497788
Building REAL300025497789
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497789'
/scratch/stefan/7787277/working/building/REAL300025497789 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497789

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497789/0 /scratch/stefan/7787277/working/building/REAL300025497789 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 659)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/659
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2CC3C=CC2O3)C1)

`REAL300025497789.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497789.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497789/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497789 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3C=CC2O3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 12, 5, 7, 7, 6, 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, 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, 7, 17, 34, 119, 119, 119, 119, 119, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 12, 1, 17, 17, 118, 1, 1, 1, 1, 1, 4, 12, 12, 12, 12, 12, 12, 12, 1, 1] 201
rigid atoms, others: [32, 1, 43, 33, 10, 11, 12, 13, 14, 15, 42, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 229
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497789 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3C=CC2O3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 12, 5, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 12, 36, 73, 114, 201, 201, 201, 201, 201, 12, 12, 12, 12, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 12, 73, 73, 201, 12, 12, 12, 12, 12, 7, 1, 1, 1, 1, 1, 1, 1, 12, 12] 201
rigid atoms, others: [35, 36, 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, 42, 43])
total number of confs: 479
number of broken/clashed sets: 32
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497789 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3C=CC2O3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 12, 5, 7, 7, 6, 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, 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, 42, 13, 1, 1, 1, 1, 1, 1, 1, 85, 119, 119, 119, 119, 119, 171, 171, 171, 201, 201, 201, 201, 201, 201, 119, 42, 42, 1, 119, 119, 119, 119, 119, 171, 201, 201, 201, 201, 201, 201, 201, 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, 43])
total number of confs: 638
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497789 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497789
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497789/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497789
Building REAL300025497790
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497790'
/scratch/stefan/7787277/working/building/REAL300025497790 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497790

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497790/0 /scratch/stefan/7787277/working/building/REAL300025497790 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 660)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/660
`/scratch/stefan/7787277/working/3D/660' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(C)(F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497790.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497790.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497790/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497790 none CCCCC(C)(F)C(=O)NC1C=CCN(C(=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', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 15, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 187, 144, 187, 187, 144, 144, 107, 107, 107, 107, 107, 67, 30, 67, 13, 1, 1, 1, 1, 1, 1, 1, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201, 187, 187, 187, 144, 107, 107, 107, 107, 107, 30, 30, 1, 107, 107] 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: 733
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: REAL300025497790 none CCCCC(C)(F)C(=O)NC1C=CCN(C(=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', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 15, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [27, 26, 26, 13, 5, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 29, 107, 107, 107, 107, 107, 1, 27, 27, 27, 27, 27, 26, 26, 26, 26, 13, 13, 13, 5, 1, 1, 1, 1, 1, 15, 15, 107, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 291
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497790 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497790
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497790/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497790
Building REAL300025497791
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497791'
/scratch/stefan/7787277/working/building/REAL300025497791 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497791

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497791/0 /scratch/stefan/7787277/working/building/REAL300025497791 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 661)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/661
`/scratch/stefan/7787277/working/3D/661' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497791.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497791.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497791/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497791 none COC1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 10, 10, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 34, 121, 121, 121, 121, 121, 1, 15, 15, 15, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 17, 17, 121, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 241
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497791 none COC1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 121, 121, 121, 121, 121, 78, 28, 78, 13, 1, 1, 1, 1, 1, 1, 1, 121, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 169, 121, 121, 121, 121, 121, 28, 28, 1, 121, 121] 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])
total number of confs: 617
number of broken/clashed sets: 29
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497791 none COC1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need 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, 10, 10, 10, 10, 10, 30, 30, 71, 115, 201, 201, 201, 201, 201, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 10, 10, 71, 71, 201, 10, 10] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 34, 35, 36, 29, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 490
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497791 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497791
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497791/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497791
Building REAL300025497792
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497792'
/scratch/stefan/7787277/working/building/REAL300025497792 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497792

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497792/0 /scratch/stefan/7787277/working/building/REAL300025497792 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 662)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/662
`/scratch/stefan/7787277/working/3D/662' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CO1)

`REAL300025497792.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497792.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497792/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497792 none CC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 33, 76, 76, 76, 76, 76, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 19, 19, 76, 1, 1, 20, 20] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44])
total number of confs: 207
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497792 none CC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 99, 99, 99, 76, 76, 76, 76, 76, 63, 38, 63, 13, 1, 1, 1, 1, 1, 1, 1, 76, 201, 201, 201, 201, 201, 201, 201, 201, 201, 99, 76, 76, 76, 76, 76, 38, 38, 1, 76, 76, 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])
total number of confs: 648
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497792 none CC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 20, 20, 49, 49, 96, 139, 201, 201, 201, 201, 201, 20, 1, 1, 2, 2, 2, 1, 1, 1, 1, 8, 20, 20, 20, 20, 20, 96, 96, 201, 20, 20, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 43, 44, 23, 24, 28, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 559
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497792 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497792
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497792/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497792
Building REAL300025497793
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497793'
/scratch/stefan/7787277/working/building/REAL300025497793 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497793

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497793/0 /scratch/stefan/7787277/working/building/REAL300025497793 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 663)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/663
`/scratch/stefan/7787277/working/3D/663' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC3CC32)C1)

`REAL300025497793.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497793.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497793/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497793 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC3CC32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 11, 23, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 1, 4, 4, 4, 29, 29, 29, 29, 29, 29, 1, 11, 11, 74, 1, 1, 1, 1, 1, 4, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1] 201
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 14, 15, 46, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 185
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497793 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC3CC32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 29, 47, 78, 119, 201, 201, 201, 201, 201, 29, 29, 29, 29, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 29, 78, 78, 201, 29, 29, 29, 29, 29, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 201
rigid atoms, others: [35, 36, 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, 46, 47])
total number of confs: 509
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497793 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC3CC32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 39, 13, 1, 1, 1, 1, 1, 1, 1, 58, 74, 74, 74, 74, 74, 116, 116, 116, 201, 201, 201, 201, 201, 201, 74, 39, 39, 1, 74, 74, 74, 74, 74, 116, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 74, 74] 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: 640
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497793 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497793
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497793/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497793
Building REAL300025497794
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497794'
/scratch/stefan/7787277/working/building/REAL300025497794 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497794

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497794/0 /scratch/stefan/7787277/working/building/REAL300025497794 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 664)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/664
`/scratch/stefan/7787277/working/3D/664' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCC2CC21)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497794.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497794.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497794/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497794 none O=C(CC1CCC2CC21)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 24, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 13, 54, 54, 54, 54, 54, 1, 24, 24, 45, 45, 45, 45, 45, 45, 45, 45, 45, 5, 1, 1, 1, 1, 1, 6, 6, 54, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 231
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497794 none O=C(CC1CCC2CC21)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 183, 201, 201, 201, 201, 201, 54, 54, 54, 54, 54, 47, 29, 47, 13, 1, 1, 1, 1, 1, 1, 1, 54, 183, 183, 201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 54, 54, 54, 54, 54, 29, 29, 1, 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])
total number of confs: 772
number of broken/clashed sets: 59
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497794 none O=C(CC1CCC2CC21)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 6, 1, 1, 1, 1, 1, 1, 1, 27, 27, 45, 45, 45, 45, 45, 52, 52, 98, 141, 201, 201, 201, 201, 201, 45, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 45, 45, 45, 45, 45, 98, 98, 201, 45, 45] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 562
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497794 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497794
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497794/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497794
Building REAL300025497795
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497795'
/scratch/stefan/7787277/working/building/REAL300025497795 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497795

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497795/0 /scratch/stefan/7787277/working/building/REAL300025497795 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 665)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/665
`/scratch/stefan/7787277/working/3D/665' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC3CC3C2)C1)

`REAL300025497795.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497795.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497795/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497795 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC3CC3C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 19, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 18, 1, 12, 12, 60, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 14, 15, 46, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 152
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497795 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC3CC3C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 18, 44, 81, 112, 201, 201, 201, 201, 201, 18, 18, 18, 18, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 18, 81, 81, 201, 18, 18, 18, 18, 18, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [35, 36, 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, 46, 47])
total number of confs: 517
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497795 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC3CC3C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 29, 13, 1, 1, 1, 1, 1, 1, 1, 43, 60, 60, 60, 60, 60, 90, 90, 90, 201, 201, 201, 201, 201, 201, 60, 29, 29, 1, 60, 60, 60, 60, 60, 90, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 60, 60] 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: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497795 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497795
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497795/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497795
Building REAL300025497796
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497796'
/scratch/stefan/7787277/working/building/REAL300025497796 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497796

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497796/0 /scratch/stefan/7787277/working/building/REAL300025497796 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 666)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/666
`/scratch/stefan/7787277/working/3D/666' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)C(OC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497796.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497796.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497796/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497796 none CCC(C)C(OC)C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
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, 128, 174, 175, 128, 128, 81, 81, 81, 81, 81, 59, 34, 59, 13, 1, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 201, 201, 201, 201, 201, 201, 174, 175, 175, 175, 128, 81, 81, 81, 81, 81, 34, 34, 1, 81, 81] 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: 811
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: REAL300025497796 none CCC(C)C(OC)C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 11, 25, 5, 11, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 20, 81, 81, 81, 81, 81, 1, 27, 27, 27, 27, 27, 25, 25, 25, 25, 11, 12, 12, 12, 5, 1, 1, 1, 1, 1, 10, 10, 81, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 240
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497796 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497796
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497796/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497796
Building REAL300025497797
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497797'
/scratch/stefan/7787277/working/building/REAL300025497797 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497797

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497797/0 /scratch/stefan/7787277/working/building/REAL300025497797 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 667)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/667
`/scratch/stefan/7787277/working/3D/667' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497797.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497797.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497797/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497797 none COC1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 6, 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]
0  hydrogens 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, 24, 24, 24, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 29, 103, 103, 103, 103, 103, 1, 24, 37, 37, 37, 24, 24, 24, 24, 24, 24, 5, 1, 1, 1, 1, 1, 16, 16, 103, 1, 1, 24, 24] 201
rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47])
total number of confs: 263
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497797 none COC1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 103, 103, 103, 103, 103, 86, 40, 86, 13, 1, 1, 1, 1, 1, 1, 1, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 103, 103, 103, 103, 103, 40, 40, 1, 103, 103, 201, 201] 201
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 642
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497797 none COC1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', '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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 24, 24, 24, 24, 24, 53, 53, 81, 123, 201, 201, 201, 201, 201, 24, 1, 4, 4, 4, 1, 1, 1, 1, 1, 1, 8, 24, 24, 24, 24, 24, 81, 81, 201, 24, 24, 1, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 34, 46, 47, 25, 29, 30, 31] set([0, 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])
total number of confs: 507
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497797 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497797
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497797/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497797
Building REAL300025497798
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497798'
/scratch/stefan/7787277/working/building/REAL300025497798 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497798

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497798/0 /scratch/stefan/7787277/working/building/REAL300025497798 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 668)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/668
`/scratch/stefan/7787277/working/3D/668' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C(C3CC3)O2)C1)

`REAL300025497798.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497798.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497798/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025497798 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C(C3CC3)O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 16, 29, 109, 109, 109, 109, 109, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 28, 28, 5, 1, 16, 16, 109, 1, 1, 1, 1, 1, 5, 5, 28, 28, 28, 28, 28, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 10, 11, 12, 13, 14, 15, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 255
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.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: REAL300025497798 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C(C3CC3)O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 28, 52, 91, 128, 201, 201, 201, 201, 201, 28, 28, 28, 28, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 12, 28, 91, 91, 201, 28, 28, 28, 28, 28, 12, 12, 1, 1, 1, 1, 1, 28, 28] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 527
number of broken/clashed sets: 8
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497798 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C(C3CC3)O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 5, 13, 27, 43, 129, 129, 129, 129, 129, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 12, 12, 1, 5, 27, 27, 129, 5, 5, 5, 5, 5, 2, 1, 12, 12, 12, 12, 12, 5, 5] 201
rigid atoms, others: [36, 16, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 278
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497798 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C(C3CC3)O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [82, 41, 13, 1, 1, 1, 1, 1, 1, 1, 82, 109, 109, 109, 109, 109, 129, 129, 129, 129, 129, 129, 129, 201, 201, 129, 109, 41, 41, 1, 109, 109, 109, 109, 109, 129, 129, 201, 201, 201, 201, 201, 109, 109] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 689
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497798 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497798
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497798/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497798
Building REAL300025497799
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497799'
/scratch/stefan/7787277/working/building/REAL300025497799 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497799

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497799/0 /scratch/stefan/7787277/working/building/REAL300025497799 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 669)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/669
`/scratch/stefan/7787277/working/3D/669' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C[C@@H]1NC(=O)NC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497799.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497799.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497799/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497799 none O=C(C[C@@H]1NC(=O)NC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 7, 8, 1, 11, 8, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens 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, 23, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 29, 93, 93, 93, 93, 93, 1, 23, 23, 45, 45, 5, 1, 1, 1, 1, 1, 16, 16, 93, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 41, 42, 11, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 318
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497799 none O=C(C[C@@H]1NC(=O)NC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 7, 8, 1, 11, 8, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [128, 128, 128, 195, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 93, 93, 72, 28, 72, 13, 1, 1, 1, 1, 1, 1, 1, 93, 195, 195, 201, 201, 128, 93, 93, 93, 93, 93, 28, 28, 1, 93, 93] 201
rigid atoms, others: [40, 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, 41, 42])
total number of confs: 701
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497799 none O=C(C[C@@H]1NC(=O)NC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 7, 8, 1, 11, 8, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [28, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 45, 45, 45, 45, 45, 62, 62, 92, 132, 201, 201, 201, 201, 201, 45, 7, 7, 1, 1, 28, 45, 45, 45, 45, 45, 92, 92, 201, 45, 45] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 10, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 528
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497799 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497799
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497799/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497799
Building REAL300025497800
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497800'
/scratch/stefan/7787277/working/building/REAL300025497800 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497800

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497800/0 /scratch/stefan/7787277/working/building/REAL300025497800 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 670)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/670
`/scratch/stefan/7787277/working/3D/670' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3CCCN23)C1)

`REAL300025497800.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497800.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497800/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497800 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3CCCN23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 5, 7, 7, 6, 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]
0  hydrogens 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, 36, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 1, 15, 15, 126, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 15, 15, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 44, 10, 11, 12, 13, 14, 15, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 225
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497800 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3CCCN23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 5, 7, 7, 6, 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]
0  hydrogens 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, 15, 38, 73, 113, 201, 201, 201, 201, 201, 15, 15, 15, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 73, 73, 201, 15, 15, 15, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 15, 15] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 16, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44])
total number of confs: 478
number of broken/clashed sets: 36
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497800 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3CCCN23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 5, 7, 7, 6, 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]
0  hydrogens 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, 45, 13, 1, 1, 1, 1, 1, 1, 1, 90, 126, 126, 126, 126, 126, 167, 167, 167, 201, 201, 201, 201, 201, 201, 201, 126, 45, 45, 1, 126, 126, 126, 126, 126, 167, 201, 201, 201, 201, 201, 201, 201, 126, 126] 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: 569
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497800 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497800
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497800/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497800
Building REAL300025497801
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497801'
/scratch/stefan/7787277/working/building/REAL300025497801 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025497801

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497801/0 /scratch/stefan/7787277/working/building/REAL300025497801 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 671)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/671
`/scratch/stefan/7787277/working/3D/671' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCN1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497801.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497801.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497801/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497801 none C#CCN1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 12, 12, 12, 12, 6, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 32, 81, 81, 81, 81, 81, 1, 20, 20, 20, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 16, 16, 81, 1, 1] 201
rigid atoms, others: [47, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 223
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497801 none C#CCN1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
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, 192, 192, 192, 152, 192, 152, 152, 81, 81, 81, 81, 81, 58, 23, 58, 12, 1, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 192, 192, 192, 192, 192, 192, 152, 81, 81, 81, 81, 81, 23, 23, 1, 81, 81] 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, 46, 47])
total number of confs: 648
number of broken/clashed sets: 33
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497801 none C#CCN1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 29, 29, 60, 100, 192, 192, 192, 192, 192, 12, 6, 6, 6, 1, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 60, 60, 192, 12, 12] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 456
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497801 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497801/1 /scratch/stefan/7787277/working/building/REAL300025497801 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 672)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/672
`/scratch/stefan/7787277/working/3D/672' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC[N@H+]1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497801.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497801.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497801/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497801 none C#CC[N@H+]1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 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]
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: [6, 6, 6, 6, 6, 6, 6, 6, 4, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 6, 14, 14, 14, 14, 14, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 6, 6, 14, 1, 1] 16
rigid atoms, others: [48, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 45
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497801 none C#CC[N@H+]1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 14, 14, 14, 14, 14, 13, 11, 13, 7, 1, 1, 1, 1, 1, 1, 1, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 14, 14, 14, 14, 14, 11, 11, 1, 14, 14] 16
rigid atoms, others: [46, 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, 47, 48])
total number of confs: 50
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497801 none C#CC[N@H+]1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
16  conformations in input
total number of sets (complete confs): 16
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 7, 7, 11, 11, 16, 16, 16, 16, 16, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 11, 11, 16, 6, 6] 16
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 36, 37] set([0, 1, 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])
total number of confs: 61
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497801 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `2'
/scratch/stefan/7787277/working/building/REAL300025497801/2 /scratch/stefan/7787277/working/building/REAL300025497801 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 2 (index: 673)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/673
`/scratch/stefan/7787277/working/3D/673' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC[N@@H+]1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497801.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025497801.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497801/2/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: REAL300025497801 none C#CC[N@@H+]1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [25, 25, 11, 11, 11, 11, 11, 11, 5, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 21, 59, 59, 59, 59, 59, 1, 25, 25, 25, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 12, 12, 59, 1, 1] 183
rigid atoms, others: [48, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 47, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 205
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497801 none C#CC[N@@H+]1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [183, 183, 115, 115, 115, 115, 115, 115, 78, 115, 78, 78, 59, 59, 59, 59, 59, 47, 24, 47, 11, 1, 1, 1, 1, 1, 1, 1, 59, 183, 183, 183, 115, 115, 115, 115, 115, 115, 78, 59, 59, 59, 59, 59, 24, 24, 1, 59, 59] 183
rigid atoms, others: [46, 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, 47, 48])
total number of confs: 766
number of broken/clashed sets: 42
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497801 none C#CC[N@@H+]1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.1', 'C.1', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
183  conformations in input
total number of sets (complete confs): 183
using faster count positions algorithm for large data
unique positions, atoms: [6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 18, 18, 27, 50, 115, 115, 115, 115, 115, 11, 6, 6, 6, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 27, 27, 115, 11, 11] 183
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 36, 37] set([0, 1, 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])
total number of confs: 247
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497801 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497801
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497801/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497801/1.*
2: /scratch/stefan/7787277/working/building/REAL300025497801/2.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497801
Building REAL300025497802
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497802'
/scratch/stefan/7787277/working/building/REAL300025497802 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497802

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497802/0 /scratch/stefan/7787277/working/building/REAL300025497802 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 674)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/674
`/scratch/stefan/7787277/working/3D/674' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=NC=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497802.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497802.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497802/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497802 none CC1=CC=NC=C1CC(=O)NC1C=CCN(C(=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.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens 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, 48, 29, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 11, 45, 45, 45, 45, 45, 1, 48, 48, 48, 48, 48, 48, 29, 29, 5, 1, 1, 1, 1, 1, 6, 6, 45, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 44, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 202
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497802 none CC1=CC=NC=C1CC(=O)NC1C=CCN(C(=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.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 160, 69, 69, 69, 45, 45, 45, 45, 45, 36, 25, 36, 12, 1, 1, 1, 1, 1, 1, 1, 45, 201, 201, 201, 201, 201, 201, 160, 160, 69, 45, 45, 45, 45, 45, 25, 25, 1, 45, 45] 201
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, 44, 45])
total number of confs: 680
number of broken/clashed sets: 50
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497802 none CC1=CC=NC=C1CC(=O)NC1C=CCN(C(=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.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 23, 23, 23, 48, 48, 48, 48, 48, 63, 63, 91, 132, 201, 201, 201, 201, 201, 48, 2, 2, 2, 1, 1, 1, 5, 5, 23, 48, 48, 48, 48, 48, 91, 91, 201, 48, 48] 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: 542
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497802 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497802
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497802/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497802
Building REAL300025497803
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497803'
/scratch/stefan/7787277/working/building/REAL300025497803 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497803

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497803/0 /scratch/stefan/7787277/working/building/REAL300025497803 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 675)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/675
`/scratch/stefan/7787277/working/3D/675' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497803.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497803.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497803/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497803 none C[C@@H]1OCCO[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 6, 11, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 35, 113, 113, 113, 113, 113, 1, 11, 11, 11, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 20, 20, 113, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 44, 11, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 235
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497803 none C[C@@H]1OCCO[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 160, 201, 160, 160, 113, 113, 113, 113, 113, 84, 41, 84, 12, 1, 1, 1, 1, 1, 1, 1, 113, 201, 201, 201, 201, 201, 201, 201, 160, 113, 113, 113, 113, 113, 41, 41, 1, 113, 113] 201
rigid atoms, others: [43, 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, 44, 45])
total number of confs: 664
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497803 none C[C@@H]1OCCO[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 4, 4, 4, 11, 11, 11, 11, 11, 38, 38, 85, 122, 201, 201, 201, 201, 201, 11, 2, 2, 2, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 85, 85, 201, 11, 11] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 32, 33, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 527
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497803 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497803
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497803/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497803
Building REAL300025497804
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497804'
/scratch/stefan/7787277/working/building/REAL300025497804 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497804

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497804/0 /scratch/stefan/7787277/working/building/REAL300025497804 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 676)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/676
`/scratch/stefan/7787277/working/3D/676' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC1=O)

`REAL300025497804.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497804.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497804/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497804 none CN1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 11, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 33, 56, 143, 143, 143, 143, 143, 1, 12, 12, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 33, 33, 143, 1, 1, 12] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42])
total number of confs: 304
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497804 none CN1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 11, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 143, 143, 143, 143, 143, 107, 44, 107, 13, 1, 1, 1, 1, 1, 1, 1, 143, 201, 201, 201, 201, 201, 201, 201, 199, 143, 143, 143, 143, 143, 44, 44, 1, 143, 143, 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])
total number of confs: 610
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497804 none CN1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 11, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 12, 12, 12, 12, 12, 33, 33, 92, 129, 201, 201, 201, 201, 201, 12, 1, 1, 1, 2, 2, 2, 1, 3, 12, 12, 12, 12, 12, 92, 92, 201, 12, 12, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 24, 25, 26, 30] set([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])
total number of confs: 549
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497804 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497804
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497804/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497804
Building REAL300025497805
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497805'
/scratch/stefan/7787277/working/building/REAL300025497805 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497805

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497805/0 /scratch/stefan/7787277/working/building/REAL300025497805 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 677)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/677
`/scratch/stefan/7787277/working/3D/677' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CNC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025497805.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497805.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497805/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497805 none CCC1=CNC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [29, 12, 12, 12, 12, 10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 15, 58, 58, 58, 58, 58, 1, 12, 29, 29, 29, 29, 29, 12, 12, 10, 10, 4, 1, 1, 1, 1, 1, 8, 8, 58, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 212
number of broken/clashed sets: 87
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497805 none CCC1=CNC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 129, 129, 129, 129, 127, 63, 63, 63, 58, 58, 58, 58, 58, 41, 28, 41, 13, 1, 1, 1, 1, 1, 1, 1, 58, 129, 201, 201, 201, 201, 201, 129, 129, 127, 127, 63, 58, 58, 58, 58, 58, 28, 28, 1, 58, 58] 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])
total number of confs: 926
number of broken/clashed sets: 87
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497805 none CCC1=CNC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [6, 1, 1, 1, 1, 1, 1, 5, 10, 10, 10, 12, 12, 12, 12, 12, 16, 16, 36, 60, 129, 129, 129, 129, 129, 12, 1, 6, 6, 6, 6, 6, 1, 1, 5, 5, 10, 12, 12, 12, 12, 12, 36, 36, 129, 12, 12] 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: 317
number of broken/clashed sets: 87
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497805 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497805
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497805/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497805
Building REAL300025497806
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497806'
/scratch/stefan/7787277/working/building/REAL300025497806 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497806

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497806/0 /scratch/stefan/7787277/working/building/REAL300025497806 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 678)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/678
`/scratch/stefan/7787277/working/3D/678' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCCC1CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497806.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497806.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497806/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497806 none C[N@@H+]1CCCC1CCC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 1, 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
4  conformations in input
total number of sets (complete confs): 4
using default count positions algorithm for smaller data
unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 4, 4, 4, 4, 4, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 1, 1, 1, 1, 3, 3, 4, 1, 1] 4
rigid atoms, others: [45, 11, 47, 44, 43, 12, 13, 14, 15, 16, 17, 51, 52, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 23
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497806 none C[N@@H+]1CCCC1CCC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 1, 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
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, 4, 4, 4, 4, 4, 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, 4, 4, 4, 4, 1, 4, 4] 4
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: 5
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497806 none C[N@@H+]1CCCC1CCC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 1, 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
4  conformations in input
total number of sets (complete confs): 4
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 3, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 4, 3, 3] 4
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 37, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 23
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497806 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497806/1 /scratch/stefan/7787277/working/building/REAL300025497806 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 679)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/679
`/scratch/stefan/7787277/working/3D/679' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCCC1CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497806.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497806.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497806/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497806 none C[N@H+]1CCCC1CCC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 1, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 5, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 10, 15, 33, 33, 33, 33, 33, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 10, 10, 33, 1, 1] 33
rigid atoms, others: [45, 11, 47, 44, 43, 12, 13, 14, 15, 16, 17, 51, 52, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 90
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497806 none C[N@H+]1CCCC1CCC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 1, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 22, 33, 12, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 22, 22, 1, 33, 33] 33
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: 103
number of broken/clashed sets: 33
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497806 none C[N@H+]1CCCC1CCC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 1, 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
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 6, 6, 6, 7, 7, 12, 17, 33, 33, 33, 33, 33, 6, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 6, 6, 6, 6, 6, 6, 12, 12, 33, 6, 6] 33
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 35, 36, 33, 37, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 88
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497806 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497806
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497806/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497806/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497806
Building REAL300025497807
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497807'
/scratch/stefan/7787277/working/building/REAL300025497807 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497807

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497807/0 /scratch/stefan/7787277/working/building/REAL300025497807 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 680)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/680
`/scratch/stefan/7787277/working/3D/680' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCNC1=O)

`REAL300025497807.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497807.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497807/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497807 none CCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCNC1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 26, 96, 96, 96, 96, 96, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 12, 12, 96, 1, 1, 11, 11, 11, 11, 11] 201
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 41, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47])
total number of confs: 186
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497807 none CCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCNC1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
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, 130, 130, 96, 96, 96, 96, 96, 76, 49, 76, 13, 1, 1, 1, 1, 1, 1, 1, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 130, 96, 96, 96, 96, 96, 49, 49, 1, 96, 96, 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])
total number of confs: 702
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497807 none CCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCNC1=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', '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', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 8, 1, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 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, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 4, 4, 11, 11, 11, 11, 11, 22, 22, 62, 100, 201, 201, 201, 201, 201, 11, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 4, 11, 11, 11, 11, 11, 62, 62, 201, 11, 11, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 2, 3, 43, 44, 45, 46, 47, 22, 23, 24, 25, 26] set([0, 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: 484
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497807 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497807
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497807/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497807
Building REAL300025497808
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497808'
/scratch/stefan/7787277/working/building/REAL300025497808 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497808

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497808/0 /scratch/stefan/7787277/working/building/REAL300025497808 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 681)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/681
`/scratch/stefan/7787277/working/3D/681' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1CCO[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497808.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497808.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497808/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497808 none CC[C@@H]1CCO[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 5, 10, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 47, 140, 140, 140, 140, 140, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 1, 27, 27, 140, 1, 1] 201
rigid atoms, others: [47, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 282
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497808 none CC[C@@H]1CCO[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 187, 201, 187, 187, 140, 140, 140, 140, 140, 107, 44, 107, 12, 1, 1, 1, 1, 1, 1, 1, 140, 201, 201, 201, 201, 201, 201, 201, 201, 201, 187, 140, 140, 140, 140, 140, 44, 44, 1, 140, 140] 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, 46, 47])
total number of confs: 623
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497808 none CC[C@@H]1CCO[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 7, 5, 5, 12, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 31, 31, 88, 120, 201, 201, 201, 201, 201, 10, 2, 2, 2, 2, 2, 1, 1, 1, 1, 4, 10, 10, 10, 10, 10, 88, 88, 201, 10, 10] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 33] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 532
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497808 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497808
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497808/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497808
Building REAL300025497809
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497809'
/scratch/stefan/7787277/working/building/REAL300025497809 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497809

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497809/0 /scratch/stefan/7787277/working/building/REAL300025497809 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 682)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/682
`/scratch/stefan/7787277/working/3D/682' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2=CNC=N2)C1)

`REAL300025497809.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497809.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497809/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025497809 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2=CNC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 7, 7, 6, 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, 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, 11, 27, 88, 88, 88, 88, 88, 1, 1, 1, 1, 1, 1, 4, 4, 4, 24, 24, 24, 24, 24, 67, 67, 67, 67, 1, 11, 11, 88, 1, 1, 1, 1, 1, 4, 24, 24, 67, 67, 67, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 36, 33, 44, 10, 11, 12, 13, 14, 15, 43, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 37, 38, 39, 40, 41, 42])
total number of confs: 263
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.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: REAL300025497809 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2=CNC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 7, 7, 6, 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, 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: [91, 67, 91, 110, 142, 201, 201, 201, 201, 201, 67, 67, 67, 67, 46, 46, 9, 46, 9, 9, 9, 1, 9, 1, 1, 1, 1, 1, 67, 110, 110, 201, 67, 67, 67, 67, 67, 46, 9, 9, 1, 1, 1, 67, 67] 201
rigid atoms, others: [40, 41, 42, 21, 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, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44])
total number of confs: 526
number of broken/clashed sets: 3
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497809 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2=CNC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 7, 7, 6, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 24, 52, 68, 106, 191, 191, 191, 191, 191, 24, 24, 24, 24, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 24, 68, 68, 191, 24, 24, 24, 24, 24, 11, 1, 1, 9, 9, 9, 24, 24] 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])
total number of confs: 452
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497809 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2=CNC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 7, 7, 6, 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, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [81, 36, 12, 1, 1, 1, 1, 1, 1, 1, 81, 88, 88, 88, 88, 88, 113, 113, 113, 191, 191, 191, 191, 191, 201, 201, 201, 201, 88, 36, 36, 1, 88, 88, 88, 88, 88, 113, 191, 191, 201, 201, 201, 88, 88] 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])
total number of confs: 635
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497809 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497809/1 /scratch/stefan/7787277/working/building/REAL300025497809 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 683)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/683
`/scratch/stefan/7787277/working/3D/683' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2=CN=CN2)C1)

`REAL300025497809.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497809.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497809/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window 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: REAL300025497809 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2=CN=CN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 17, 31, 96, 96, 96, 96, 96, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 28, 28, 28, 28, 1, 17, 17, 96, 1, 1, 1, 1, 1, 5, 17, 17, 28, 28, 28, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 36, 33, 44, 10, 11, 12, 13, 14, 15, 43, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 37, 38, 39, 40, 41, 42])
total number of confs: 237
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: REAL300025497809 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2=CN=CN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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: [63, 28, 63, 91, 130, 201, 201, 201, 201, 201, 28, 28, 28, 28, 19, 19, 7, 19, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 28, 91, 91, 201, 28, 28, 28, 28, 28, 19, 7, 7, 1, 1, 1, 28, 28] 201
rigid atoms, others: [40, 41, 42, 21, 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, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44])
total number of confs: 521
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497809 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2=CN=CN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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: [46, 17, 46, 73, 111, 190, 190, 190, 190, 190, 17, 17, 17, 17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 17, 73, 73, 190, 17, 17, 17, 17, 17, 9, 1, 1, 7, 7, 7, 17, 17] 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])
total number of confs: 479
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497809 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2=CN=CN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 8, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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: [86, 42, 12, 1, 1, 1, 1, 1, 1, 1, 86, 96, 96, 96, 96, 96, 115, 115, 115, 190, 190, 190, 190, 190, 201, 201, 201, 201, 96, 42, 42, 1, 96, 96, 96, 96, 96, 115, 190, 190, 201, 201, 201, 96, 96] 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])
total number of confs: 615
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497809 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497809
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497809/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497809/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497809
Building REAL300025497810
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497810'
/scratch/stefan/7787277/working/building/REAL300025497810 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497810

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497810/0 /scratch/stefan/7787277/working/building/REAL300025497810 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 684)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/684
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2CCC=CCCC2)C1)

`REAL300025497810.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497810.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497810/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497810 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC=CCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [5, 1, 5, 17, 30, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 1, 17, 17, 76, 1, 1, 1, 1, 1, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 49, 50, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 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])
total number of confs: 207
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497810 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC=CCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [48, 21, 48, 98, 139, 201, 201, 201, 201, 201, 21, 21, 21, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 21, 98, 98, 201, 21, 21, 21, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 201
rigid atoms, others: [16, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 49, 50])
total number of confs: 567
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497810 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC=CCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [63, 39, 13, 1, 1, 1, 1, 1, 1, 1, 63, 76, 76, 76, 76, 76, 103, 103, 103, 201, 201, 201, 201, 201, 201, 201, 76, 39, 39, 1, 76, 76, 76, 76, 76, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 76, 76] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 652
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497810 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497810
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497810/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497810
Building REAL300025497811
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497811'
/scratch/stefan/7787277/working/building/REAL300025497811 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497811

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497811/0 /scratch/stefan/7787277/working/building/REAL300025497811 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 685)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/685
`/scratch/stefan/7787277/working/3D/685' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1C1CC1)

`REAL300025497811.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497811.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497811/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025497811 none CC1C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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: [10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 37, 123, 123, 123, 123, 123, 1, 10, 10, 14, 14, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 1, 19, 19, 123, 1, 1, 10, 14, 14, 14, 14, 14] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 41] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47])
total number of confs: 258
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL300025497811 none CC1C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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: [4, 4, 4, 4, 6, 6, 6, 14, 14, 14, 14, 14, 36, 36, 75, 116, 201, 201, 201, 201, 201, 14, 1, 1, 1, 1, 4, 4, 4, 4, 4, 6, 14, 14, 14, 14, 14, 75, 75, 201, 14, 14, 4, 1, 1, 1, 1, 1] 201
rigid atoms, others: [43, 44, 45, 46, 47, 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])
total number of confs: 498
number of broken/clashed sets: 43
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497811 none CC1C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 163, 163, 163, 123, 123, 123, 123, 123, 76, 31, 76, 13, 1, 1, 1, 1, 1, 1, 1, 123, 201, 201, 201, 201, 201, 201, 201, 201, 201, 163, 123, 123, 123, 123, 123, 31, 31, 1, 123, 123, 201, 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: 611
number of broken/clashed sets: 43
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497811 none CC1C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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, 4, 4, 4, 10, 10, 10, 10, 10, 31, 31, 70, 112, 201, 201, 201, 201, 201, 10, 1, 1, 4, 4, 2, 2, 2, 1, 1, 4, 10, 10, 10, 10, 10, 70, 70, 201, 10, 10, 1, 4, 4, 4, 4, 4] 201
rigid atoms, others: [0, 1, 2, 3, 42, 22, 23, 29, 30] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47])
total number of confs: 501
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497811 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497811
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497811/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497811
Building REAL300025497812
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497812'
/scratch/stefan/7787277/working/building/REAL300025497812 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497812

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497812/0 /scratch/stefan/7787277/working/building/REAL300025497812 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 686)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/686
`/scratch/stefan/7787277/working/3D/686' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCNC(=O)C1)

`REAL300025497812.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497812.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497812/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497812 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCNC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', '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, 1, 1, 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, 6, 7, 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: [11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 36, 106, 106, 106, 106, 106, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 14, 14, 106, 1, 1, 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, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 208
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497812 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCNC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', '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, 1, 1, 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, 6, 7, 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, 144, 144, 144, 106, 106, 106, 106, 106, 94, 48, 94, 13, 1, 1, 1, 1, 1, 1, 1, 106, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 106, 106, 106, 106, 106, 48, 48, 1, 106, 106, 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])
total number of confs: 674
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497812 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCNC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', '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, 1, 1, 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, 6, 7, 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, 11, 11, 11, 11, 11, 28, 28, 57, 104, 201, 201, 201, 201, 201, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 11, 11, 11, 11, 11, 57, 57, 201, 11, 11, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 41, 42, 43, 44, 45, 46, 47, 21, 22, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 452
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497812 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497812
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497812/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497812
Building REAL300025497813
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497813'
/scratch/stefan/7787277/working/building/REAL300025497813 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497813

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497813/0 /scratch/stefan/7787277/working/building/REAL300025497813 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 687)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/687
`/scratch/stefan/7787277/working/3D/687' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC23CC3)C1)

`REAL300025497813.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497813.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497813/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497813 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC23CC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 94, 94, 94, 94, 94, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 11, 1, 15, 15, 94, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1] 201
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 14, 15, 46, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 193
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497813 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC23CC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 11, 33, 64, 97, 201, 201, 201, 201, 201, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 11, 64, 64, 201, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 201
rigid atoms, others: [35, 36, 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, 46, 47])
total number of confs: 460
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497813 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCC23CC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 94, 94, 94, 94, 94, 138, 138, 138, 201, 201, 201, 201, 201, 201, 94, 39, 39, 1, 94, 94, 94, 94, 94, 138, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 94, 94] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 697
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497813 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497813
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497813/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497813
Building REAL300025497814
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497814'
/scratch/stefan/7787277/working/building/REAL300025497814 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497814

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497814/0 /scratch/stefan/7787277/working/building/REAL300025497814 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 688)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/688
`/scratch/stefan/7787277/working/3D/688' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1CCCC1(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497814.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497814.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497814/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497814 none CCC1CCCC1(C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens 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, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 41, 114, 114, 114, 114, 114, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 24, 24, 114, 1, 1] 201
rigid atoms, others: [11, 47, 44, 10, 43, 12, 13, 14, 45, 16, 51, 52, 46, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 253
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497814 none CCC1CCCC1(C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 193, 201, 193, 193, 114, 114, 114, 114, 114, 85, 41, 85, 13, 1, 1, 1, 1, 1, 1, 1, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 114, 114, 114, 114, 114, 41, 41, 1, 114, 114] 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: 604
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497814 none CCC1CCCC1(C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 34, 34, 76, 113, 201, 201, 201, 201, 201, 12, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 12, 12, 12, 12, 12, 76, 76, 201, 12, 12] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 8, 7, 34, 35, 36, 38, 37] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 507
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497814 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497814
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497814/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497814
Building REAL300025497815
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497815'
/scratch/stefan/7787277/working/building/REAL300025497815 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497815

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497815/0 /scratch/stefan/7787277/working/building/REAL300025497815 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 689)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/689
`/scratch/stefan/7787277/working/3D/689' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCOCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497815.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497815.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497815/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497815 none COCCOCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 173, 161, 141, 141, 50, 50, 50, 36, 36, 36, 36, 36, 36, 27, 36, 13, 1, 1, 1, 1, 1, 1, 1, 36, 201, 201, 201, 201, 201, 173, 173, 141, 141, 141, 141, 50, 36, 36, 36, 36, 36, 27, 27, 1, 36, 36] 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])
total number of confs: 789
number of broken/clashed sets: 157
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497815 none COCCOCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 37, 28, 20, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 6, 36, 36, 36, 36, 36, 1, 40, 40, 40, 37, 37, 28, 28, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 4, 4, 36, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 194
number of broken/clashed sets: 157
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497815 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497815
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497815/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497815
Building REAL300025497816
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497816'
/scratch/stefan/7787277/working/building/REAL300025497816 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497816

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497816/0 /scratch/stefan/7787277/working/building/REAL300025497816 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 690)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/690
`/scratch/stefan/7787277/working/3D/690' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCCCC1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497816.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497816.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497816/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497816 none CC1CCCCC1CC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens 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, 22, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 25, 98, 98, 98, 98, 98, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 16, 16, 5, 1, 1, 1, 1, 1, 14, 14, 98, 1, 1] 201
rigid atoms, others: [11, 47, 44, 10, 43, 12, 13, 14, 45, 16, 51, 52, 46, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 243
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497816 none CC1CCCCC1CC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens need rotated
201  conformations in input
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, 130, 130, 130, 98, 98, 98, 98, 98, 60, 30, 60, 13, 1, 1, 1, 1, 1, 1, 1, 98, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 130, 98, 98, 98, 98, 98, 30, 30, 1, 98, 98] 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: 761
number of broken/clashed sets: 54
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497816 none CC1CCCCC1CC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens need rotated
201  conformations in input
total 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, 13, 13, 13, 23, 23, 23, 23, 23, 44, 44, 80, 119, 201, 201, 201, 201, 201, 23, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 23, 23, 23, 23, 23, 80, 80, 201, 23, 23] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 39, 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, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 529
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497816 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497816
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497816/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497816
Building REAL300025497817
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497817'
/scratch/stefan/7787277/working/building/REAL300025497817 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497817

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497817/0 /scratch/stefan/7787277/working/building/REAL300025497817 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 691)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/691
`/scratch/stefan/7787277/working/3D/691' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CC=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497817.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497817.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497817/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497817 none O=C(CCC1=CC=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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: [5, 5, 5, 19, 23, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 78, 78, 78, 78, 78, 1, 19, 19, 23, 23, 31, 31, 31, 31, 5, 1, 1, 1, 1, 1, 10, 10, 78, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 44, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 227
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497817 none O=C(CCC1=CC=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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: [116, 116, 116, 187, 201, 201, 201, 201, 201, 201, 78, 78, 78, 78, 78, 56, 30, 56, 13, 1, 1, 1, 1, 1, 1, 1, 78, 187, 187, 201, 201, 201, 201, 201, 201, 116, 78, 78, 78, 78, 78, 30, 30, 1, 78, 78] 201
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, 44, 45])
total number of confs: 755
number of broken/clashed sets: 66
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497817 none O=C(CCC1=CC=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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: [19, 10, 6, 1, 1, 1, 1, 1, 1, 1, 19, 19, 31, 31, 31, 31, 31, 41, 41, 75, 119, 201, 201, 201, 201, 201, 31, 10, 10, 6, 6, 1, 1, 1, 1, 19, 31, 31, 31, 31, 31, 75, 75, 201, 31, 31] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 534
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497817 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497817
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497817/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497817
Building REAL300025497818
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497818'
/scratch/stefan/7787277/working/building/REAL300025497818 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497818

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497818/0 /scratch/stefan/7787277/working/building/REAL300025497818 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 692)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/692
`/scratch/stefan/7787277/working/3D/692' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CSC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497818.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497818.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497818/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497818 none O=C(CCC1=CSC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 24, 31, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 52, 52, 52, 52, 52, 1, 24, 24, 31, 31, 46, 46, 5, 1, 1, 1, 1, 1, 6, 6, 52, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 227
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497818 none O=C(CCC1=CSC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [89, 89, 89, 179, 181, 201, 201, 201, 201, 52, 52, 52, 52, 52, 42, 26, 42, 12, 1, 1, 1, 1, 1, 1, 1, 52, 179, 179, 181, 181, 201, 201, 89, 52, 52, 52, 52, 52, 26, 26, 1, 52, 52] 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])
total number of confs: 723
number of broken/clashed sets: 50
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497818 none O=C(CCC1=CSC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 14, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 27, 27, 46, 46, 46, 46, 46, 55, 55, 94, 129, 201, 201, 201, 201, 201, 46, 9, 9, 4, 4, 1, 1, 27, 46, 46, 46, 46, 46, 94, 94, 201, 46, 46] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 557
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497818 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497818
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497818/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497818
Building REAL300025497819
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497819'
/scratch/stefan/7787277/working/building/REAL300025497819 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497819

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497819/0 /scratch/stefan/7787277/working/building/REAL300025497819 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 693)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/693
`/scratch/stefan/7787277/working/3D/693' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCN1C=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497819.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497819.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497819/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497819 none O=C(CCCN1C=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 9, 5, 11, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 44, 44, 44, 44, 44, 1, 9, 9, 9, 9, 9, 9, 19, 19, 19, 2, 1, 1, 1, 1, 1, 5, 5, 44, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 139
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497819 none O=C(CCCN1C=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 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]
0  hydrogens 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, 127, 102, 133, 201, 201, 201, 201, 44, 44, 44, 44, 44, 34, 26, 34, 13, 1, 1, 1, 1, 1, 1, 1, 44, 127, 127, 127, 127, 122, 128, 201, 201, 201, 44, 44, 44, 44, 44, 44, 26, 26, 1, 44, 44] 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])
total number of confs: 782
number of broken/clashed sets: 78
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497819 none O=C(CCCN1C=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 8, 1, 1, 8, 1, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 9, 7, 6, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 29, 29, 59, 104, 201, 201, 201, 201, 201, 19, 9, 9, 7, 7, 6, 6, 1, 1, 1, 19, 19, 19, 19, 19, 19, 59, 59, 201, 19, 19] 201
rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 490
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497819 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497819
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497819/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497819
Building REAL300025497820
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497820'
/scratch/stefan/7787277/working/building/REAL300025497820 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497820

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497820/0 /scratch/stefan/7787277/working/building/REAL300025497820 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 694)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/694
`/scratch/stefan/7787277/working/3D/694' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)OCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497820.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497820.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497820/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497820 none CC(C)OCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 144, 121, 132, 58, 58, 58, 58, 58, 58, 58, 58, 47, 26, 47, 13, 1, 1, 1, 1, 1, 1, 1, 58, 201, 201, 201, 201, 201, 201, 201, 128, 137, 144, 144, 132, 132, 58, 58, 58, 58, 58, 58, 26, 26, 1, 58, 58] 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: 762
number of broken/clashed sets: 141
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497820 none CC(C)OCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [38, 29, 38, 18, 14, 10, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 18, 58, 58, 58, 58, 58, 1, 38, 38, 38, 38, 38, 38, 38, 16, 16, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 8, 8, 58, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 261
number of broken/clashed sets: 141
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497820 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497820
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497820/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497820
Building REAL300025497821
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497821'
/scratch/stefan/7787277/working/building/REAL300025497821 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497821

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497821/0 /scratch/stefan/7787277/working/building/REAL300025497821 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 695)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/695
`/scratch/stefan/7787277/working/3D/695' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497821.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497821.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497821/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497821 none NC(=O)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  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, 165, 67, 67, 67, 58, 58, 58, 58, 58, 48, 28, 48, 13, 1, 1, 1, 1, 1, 1, 1, 58, 201, 201, 188, 191, 182, 182, 165, 165, 67, 58, 58, 58, 58, 58, 28, 28, 1, 58, 58] 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])
total number of confs: 943
number of broken/clashed sets: 158
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497821 none NC(=O)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 32, 36, 16, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 16, 58, 58, 58, 58, 58, 1, 36, 36, 29, 30, 20, 20, 13, 13, 4, 1, 1, 1, 1, 1, 9, 9, 58, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 271
number of broken/clashed sets: 158
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497821 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497821
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497821/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497821
Building REAL300025497822
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497822'
/scratch/stefan/7787277/working/building/REAL300025497822 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497822

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497822/0 /scratch/stefan/7787277/working/building/REAL300025497822 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 696)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/696
`/scratch/stefan/7787277/working/3D/696' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+]1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1)

`REAL300025497822.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497822.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497822/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497822 none C[NH+]1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
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: [15, 15, 15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9, 13, 24, 24, 24, 24, 24, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 9, 9, 24, 1, 1, 15, 15, 15, 15] 61
rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49])
total number of confs: 93
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497822 none C[NH+]1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
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, 34, 34, 34, 24, 24, 24, 24, 24, 24, 21, 24, 11, 1, 1, 1, 1, 1, 1, 1, 24, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 34, 24, 24, 24, 24, 24, 21, 21, 1, 24, 24, 61, 61, 61, 61] 61
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49])
total number of confs: 200
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497822 none C[NH+]1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
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, 7, 7, 7, 15, 15, 15, 15, 15, 30, 30, 43, 53, 61, 61, 61, 61, 61, 15, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 43, 43, 61, 15, 15, 1, 1, 1, 1] 61
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 46, 47, 33, 49, 48, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 203
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497822 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497822
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497822/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497822
Building REAL300025497823
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497823'
/scratch/stefan/7787277/working/building/REAL300025497823 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497823

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497823/0 /scratch/stefan/7787277/working/building/REAL300025497823 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 697)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/697
`/scratch/stefan/7787277/working/3D/697' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COC3=CC=CC=C23)C1)

`REAL300025497823.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497823.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497823/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497823 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COC3=CC=CC=C23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 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, 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: [6, 1, 6, 19, 33, 92, 92, 92, 92, 92, 1, 1, 1, 1, 1, 1, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 1, 19, 19, 92, 1, 1, 1, 1, 1, 5, 21, 21, 21, 21, 21, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 207
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497823 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COC3=CC=CC=C23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [54, 21, 54, 98, 138, 201, 201, 201, 201, 201, 21, 21, 21, 21, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 98, 98, 201, 21, 21, 21, 21, 21, 6, 1, 1, 1, 1, 1, 21, 21] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 552
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497823 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=COC3=CC=CC=C23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 12, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 39, 13, 1, 1, 1, 1, 1, 1, 1, 74, 92, 92, 92, 92, 92, 126, 126, 126, 201, 201, 201, 201, 201, 201, 201, 201, 92, 39, 39, 1, 92, 92, 92, 92, 92, 126, 201, 201, 201, 201, 201, 92, 92] 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: 525
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497823 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497823
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497823/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497823
Building REAL300025497824
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497824'
/scratch/stefan/7787277/working/building/REAL300025497824 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497824

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497824/0 /scratch/stefan/7787277/working/building/REAL300025497824 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 698)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/698
`/scratch/stefan/7787277/working/3D/698' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)N1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497824.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497824.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497824/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497824 none NC(=O)N1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 14, 17, 14, 14, 14, 14, 5, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 35, 113, 113, 113, 113, 112, 1, 17, 17, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 19, 19, 113, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 11, 12, 13, 14, 15, 16, 17, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 241
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497824 none NC(=O)N1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 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]
0  hydrogens need 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, 201, 194, 194, 194, 194, 159, 194, 159, 159, 112, 112, 112, 113, 112, 67, 27, 67, 11, 1, 1, 1, 1, 1, 1, 1, 112, 201, 201, 194, 194, 194, 194, 194, 194, 159, 112, 113, 113, 113, 113, 27, 27, 1, 112, 112] 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, 45, 46])
total number of confs: 636
number of broken/clashed sets: 61
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497824 none NC(=O)N1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 14, 14, 14, 42, 42, 72, 111, 194, 194, 194, 194, 194, 14, 3, 3, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 14, 14, 72, 72, 194, 14, 14] 201
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 35, 33, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 467
number of broken/clashed sets: 61
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497824 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497824
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497824/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497824
Building REAL300025497825
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497825'
/scratch/stefan/7787277/working/building/REAL300025497825 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497825

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497825/0 /scratch/stefan/7787277/working/building/REAL300025497825 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 699)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/699
`/scratch/stefan/7787277/working/3D/699' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=CC(F)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497825.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497825.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497825/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497825 none CC1=CC=CC(F)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens 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, 8, 25, 25, 25, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 33, 100, 100, 100, 100, 100, 1, 25, 25, 25, 25, 25, 25, 5, 1, 1, 1, 1, 1, 18, 18, 100, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 274
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497825 none CC1=CC=CC(F)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
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, 129, 129, 129, 100, 100, 100, 100, 100, 79, 39, 79, 13, 1, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 201, 201, 129, 100, 100, 100, 100, 100, 39, 39, 1, 100, 100] 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, 42, 43])
total number of confs: 536
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497825 none CC1=CC=CC(F)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 15, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 25, 25, 25, 25, 25, 54, 54, 98, 145, 201, 201, 201, 201, 201, 25, 2, 2, 2, 1, 1, 1, 8, 25, 25, 25, 25, 25, 98, 98, 201, 25, 25] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 580
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497825 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497825
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497825/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497825
Building REAL300025497826
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497826'
/scratch/stefan/7787277/working/building/REAL300025497826 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497826

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497826/0 /scratch/stefan/7787277/working/building/REAL300025497826 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 700)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/700
`/scratch/stefan/7787277/working/3D/700' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COCC1CCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497826.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497826.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497826/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497826 none O=C(COCC1CCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 6, 16, 27, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 17, 58, 58, 58, 58, 58, 1, 6, 6, 27, 27, 38, 38, 38, 38, 38, 38, 38, 2, 1, 1, 1, 1, 1, 8, 8, 58, 1, 1] 201
rigid atoms, others: [48, 43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 228
number of broken/clashed sets: 122
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497826 none O=C(COCC1CCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [58, 58, 58, 142, 176, 193, 201, 201, 201, 201, 58, 58, 58, 58, 58, 47, 27, 47, 13, 1, 1, 1, 1, 1, 1, 1, 58, 142, 142, 193, 193, 201, 201, 201, 201, 201, 201, 201, 58, 58, 58, 58, 58, 58, 27, 27, 1, 58, 58] 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])
total number of confs: 730
number of broken/clashed sets: 122
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497826 none O=C(COCC1CCCO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 5, 5, 5, 12, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 7, 3, 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]
0  hydrogens 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, 12, 5, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 41, 41, 64, 107, 201, 201, 201, 201, 201, 38, 26, 26, 5, 5, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 64, 64, 201, 38, 38] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 36, 37, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 494
number of broken/clashed sets: 122
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497826 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497826
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497826/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497826
Building REAL300025497827
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497827'
/scratch/stefan/7787277/working/building/REAL300025497827 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497827

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497827/0 /scratch/stefan/7787277/working/building/REAL300025497827 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 701)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/701
`/scratch/stefan/7787277/working/3D/701' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1C)

`REAL300025497827.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497827.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497827/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497827 none CCC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 5, 5, 5, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 35, 83, 83, 83, 83, 83, 1, 5, 5, 5, 9, 9, 9, 9, 9, 5, 4, 1, 1, 1, 1, 1, 20, 20, 83, 1, 1, 5, 5, 5] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46])
total number of confs: 211
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497827 none CCC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 106, 106, 106, 106, 106, 106, 83, 83, 83, 83, 83, 67, 35, 67, 13, 1, 1, 1, 1, 1, 1, 1, 83, 106, 106, 106, 201, 201, 201, 201, 201, 106, 106, 83, 83, 83, 83, 83, 35, 35, 1, 83, 83, 106, 106, 106] 201
rigid atoms, others: [41, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46])
total number of confs: 911
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497827 none CCC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 2, 2, 2, 5, 5, 5, 5, 5, 19, 19, 45, 64, 106, 106, 106, 106, 106, 5, 1, 1, 1, 3, 3, 3, 3, 3, 1, 2, 5, 5, 5, 5, 5, 45, 45, 106, 5, 5, 2, 2, 2] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 24, 25, 26] set([0, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 295
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497827 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497827
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497827/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497827
Building REAL300025497828
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497828'
/scratch/stefan/7787277/working/building/REAL300025497828 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497828

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497828/0 /scratch/stefan/7787277/working/building/REAL300025497828 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 702)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/702
`/scratch/stefan/7787277/working/3D/702' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1N=C(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025497828.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497828.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497828/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497828 none CCN1N=C(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [17, 7, 7, 7, 7, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 32, 98, 98, 98, 98, 98, 1, 7, 17, 17, 17, 17, 17, 7, 7, 7, 5, 1, 1, 1, 1, 1, 19, 19, 98, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 248
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497828 none CCN1N=C(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 124, 124, 124, 124, 124, 123, 123, 123, 98, 98, 98, 98, 98, 79, 40, 79, 13, 1, 1, 1, 1, 1, 1, 1, 98, 124, 201, 201, 201, 201, 201, 124, 124, 124, 123, 98, 98, 98, 98, 98, 40, 40, 1, 98, 98] 201
rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45])
total number of confs: 860
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497828 none CCN1N=C(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 22, 22, 45, 68, 124, 124, 124, 124, 124, 7, 1, 7, 7, 7, 7, 7, 2, 2, 2, 3, 7, 7, 7, 7, 7, 45, 45, 124, 7, 7] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 329
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497828 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497828
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497828/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497828
Building REAL300025497829
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497829'
/scratch/stefan/7787277/working/building/REAL300025497829 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497829

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497829/0 /scratch/stefan/7787277/working/building/REAL300025497829 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 703)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/703
`/scratch/stefan/7787277/working/3D/703' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1)

`REAL300025497829.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497829.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497829/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497829 none CN1C=C(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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: [22, 22, 22, 19, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 29, 110, 110, 110, 110, 110, 1, 22, 22, 22, 22, 22, 22, 19, 19, 16, 16, 5, 1, 1, 1, 1, 1, 17, 17, 110, 1, 1] 192
rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 261
number of broken/clashed sets: 69
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497829 none CN1C=C(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
192  conformations in input
total number of sets (complete confs): 192
using faster count positions algorithm for large data
unique positions, atoms: [192, 192, 192, 192, 186, 136, 136, 136, 110, 110, 110, 110, 110, 75, 31, 75, 13, 1, 1, 1, 1, 1, 1, 1, 110, 192, 192, 192, 192, 192, 192, 192, 192, 186, 186, 136, 110, 110, 110, 110, 110, 31, 31, 1, 110, 110] 192
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])
total number of confs: 656
number of broken/clashed sets: 69
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497829 none CN1C=C(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 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, 1, 1, 5, 9, 13, 13, 13, 22, 22, 22, 22, 22, 29, 29, 69, 106, 192, 192, 192, 192, 192, 22, 1, 1, 2, 2, 2, 1, 5, 5, 9, 9, 13, 22, 22, 22, 22, 22, 69, 69, 192, 22, 22] 192
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: 502
number of broken/clashed sets: 69
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497829 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497829
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497829/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497829
Building REAL300025497830
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497830'
/scratch/stefan/7787277/working/building/REAL300025497830 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497830

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497830/0 /scratch/stefan/7787277/working/building/REAL300025497830 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 704)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/704
`/scratch/stefan/7787277/working/3D/704' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(C(N)=O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497830.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497830.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497830/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497830 none CC(C)CC(C(N)=O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 137, 201, 201, 201, 137, 137, 87, 87, 87, 87, 87, 57, 33, 57, 13, 1, 1, 1, 1, 1, 1, 1, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 137, 87, 87, 87, 87, 87, 33, 33, 1, 87, 87] 201
rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49])
total number of confs: 786
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: REAL300025497830 none CC(C)CC(C(N)=O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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, 7]
0  hydrogens 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, 14, 5, 14, 24, 24, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 18, 87, 87, 87, 87, 87, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 14, 24, 24, 5, 1, 1, 1, 1, 1, 9, 9, 87, 1, 1] 201
rigid atoms, others: [48, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 218
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497830 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497830
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497830/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497830
Building REAL300025497831
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497831'
/scratch/stefan/7787277/working/building/REAL300025497831 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497831

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497831/0 /scratch/stefan/7787277/working/building/REAL300025497831 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 705)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/705
`/scratch/stefan/7787277/working/3D/705' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC1CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497831.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497831.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497831/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497831 none CCCC1CCCC1C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 7, 7, 7, 7, 7, 7, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 41, 143, 143, 143, 143, 143, 1, 10, 10, 10, 10, 10, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 1, 21, 21, 143, 1, 1] 201
rigid atoms, others: [11, 47, 44, 10, 43, 12, 13, 14, 45, 16, 51, 52, 46, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 274
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497831 none CCCC1CCCC1C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 198, 198, 198, 143, 143, 143, 143, 143, 93, 31, 93, 13, 1, 1, 1, 1, 1, 1, 1, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 198, 143, 143, 143, 143, 143, 31, 31, 1, 143, 143] 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: 573
number of broken/clashed sets: 39
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497831 none CCCC1CCCC1C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 23, 23, 65, 106, 201, 201, 201, 201, 201, 7, 3, 3, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 65, 65, 201, 7, 7] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 40, 41, 39, 34, 8, 35, 36, 38, 37] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 473
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497831 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497831
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497831/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497831
Building REAL300025497832
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497832'
/scratch/stefan/7787277/working/building/REAL300025497832 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497832

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497832/0 /scratch/stefan/7787277/working/building/REAL300025497832 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 706)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/706
`/scratch/stefan/7787277/working/3D/706' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC)C(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497832.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497832.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497832/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497832 none CCC(CC)C(C)C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 149, 148, 149, 201, 64, 148, 64, 64, 42, 42, 42, 42, 42, 31, 21, 31, 11, 1, 1, 1, 1, 1, 1, 1, 42, 201, 201, 201, 201, 201, 149, 201, 201, 201, 201, 201, 148, 148, 148, 148, 64, 42, 42, 42, 42, 42, 21, 21, 1, 42, 42] 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])
total number of confs: 1195
number of broken/clashed sets: 64
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497832 none CCC(CC)C(C)C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [31, 24, 20, 21, 31, 5, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 15, 42, 42, 42, 42, 42, 1, 31, 31, 31, 31, 31, 24, 28, 31, 31, 31, 31, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 8, 8, 42, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49])
total number of confs: 258
number of broken/clashed sets: 64
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497832 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497832
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497832/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497832
Building REAL300025497833
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497833'
/scratch/stefan/7787277/working/building/REAL300025497833 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497833

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497833/0 /scratch/stefan/7787277/working/building/REAL300025497833 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 707)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/707
`/scratch/stefan/7787277/working/3D/707' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NN(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O)

`REAL300025497833.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497833.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497833/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497833 none CN1C=NN(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 27, 27, 27, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 87, 87, 87, 87, 87, 1, 27, 27, 27, 27, 27, 27, 15, 15, 5, 1, 1, 1, 1, 1, 12, 12, 87, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 208
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497833 none CN1C=NN(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 186, 115, 115, 115, 87, 87, 87, 87, 87, 50, 29, 50, 13, 1, 1, 1, 1, 1, 1, 1, 87, 201, 201, 201, 201, 201, 201, 186, 186, 115, 87, 87, 87, 87, 87, 29, 29, 1, 87, 87] 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])
total number of confs: 711
number of broken/clashed sets: 48
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497833 none CN1C=NN(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'N.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 8, 8, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
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, 16, 16, 16, 27, 27, 27, 27, 27, 42, 42, 74, 112, 201, 201, 201, 201, 201, 27, 1, 1, 2, 2, 2, 1, 5, 5, 16, 27, 27, 27, 27, 27, 74, 74, 201, 27, 27] 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])
total number of confs: 522
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497833 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497833
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497833/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497833
Building REAL300025497834
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497834'
/scratch/stefan/7787277/working/building/REAL300025497834 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497834

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497834/0 /scratch/stefan/7787277/working/building/REAL300025497834 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 708)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/708
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2=CN=C3C=CC=CN23)C1)

`REAL300025497834.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497834.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497834/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497834 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3C=CC=CN23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 7, 7, 6, 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, 24, 41, 138, 138, 138, 138, 138, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 19, 19, 19, 19, 19, 1, 24, 24, 138, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 275
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497834 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3C=CC=CN23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 7, 7, 6, 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: [49, 19, 49, 100, 131, 201, 201, 201, 201, 201, 19, 19, 19, 19, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 100, 100, 201, 19, 19, 19, 19, 19, 7, 1, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 575
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497834 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=C3C=CC=CN23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 8, 5, 7, 7, 6, 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: [100, 45, 13, 1, 1, 1, 1, 1, 1, 1, 100, 138, 138, 138, 138, 138, 185, 185, 185, 201, 201, 201, 201, 201, 201, 201, 201, 138, 45, 45, 1, 138, 138, 138, 138, 138, 185, 201, 201, 201, 201, 201, 138, 138] 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: 598
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497834 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497834
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497834/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497834
Building REAL300025497835
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497835'
/scratch/stefan/7787277/working/building/REAL300025497835 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497835

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497835/0 /scratch/stefan/7787277/working/building/REAL300025497835 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 709)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/709
`/scratch/stefan/7787277/working/3D/709' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CN=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497835.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497835.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497835/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497835 none CCC1=CN=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens 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, 17, 17, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 72, 72, 72, 72, 72, 1, 28, 28, 28, 28, 28, 17, 17, 17, 5, 1, 1, 1, 1, 1, 12, 12, 72, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 44, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 216
number of broken/clashed sets: 56
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497835 none CCC1=CN=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need 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, 149, 149, 149, 96, 96, 96, 72, 72, 72, 72, 72, 43, 26, 43, 12, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 201, 149, 149, 149, 96, 72, 72, 72, 72, 72, 26, 26, 1, 72, 72] 201
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, 44, 45])
total number of confs: 683
number of broken/clashed sets: 56
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497835 none CCC1=CN=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 17, 17, 31, 31, 52, 78, 149, 149, 149, 149, 149, 17, 3, 3, 3, 3, 3, 1, 1, 1, 7, 17, 17, 17, 17, 17, 52, 52, 149, 17, 17] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 360
number of broken/clashed sets: 56
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497835 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497835
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497835/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497835
Building REAL300025497836
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497836'
/scratch/stefan/7787277/working/building/REAL300025497836 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497836

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497836/0 /scratch/stefan/7787277/working/building/REAL300025497836 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 710)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/710
`/scratch/stefan/7787277/working/3D/710' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1CCOCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497836.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497836.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497836/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497836 none CCN1CCOCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 15, 15, 15, 15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 41, 124, 124, 124, 124, 124, 1, 19, 19, 19, 19, 19, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 23, 23, 124, 1, 1] 201
rigid atoms, others: [48, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 288
number of broken/clashed sets: 194
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497836 none CCN1CCOCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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
201  conformations in input
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, 177, 177, 177, 124, 124, 124, 124, 124, 96, 42, 96, 13, 1, 1, 1, 1, 1, 1, 1, 124, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 177, 124, 124, 124, 124, 124, 42, 42, 1, 124, 124] 201
rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49])
total number of confs: 645
number of broken/clashed sets: 194
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497836 none CCN1CCOCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 10, 5, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 38, 38, 99, 126, 201, 201, 201, 201, 201, 15, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 99, 99, 201, 15, 15] 201
rigid atoms, others: [32, 1, 2, 3, 4, 33, 6, 7, 8, 34, 35, 36, 38, 37, 5] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 559
number of broken/clashed sets: 194
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497836 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497836
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497836/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497836
Building REAL300025497837
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497837'
/scratch/stefan/7787277/working/building/REAL300025497837 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497837

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497837/0 /scratch/stefan/7787277/working/building/REAL300025497837 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 711)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/711
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2(F)CCCC2)C1)

`REAL300025497837.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497837.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497837/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497837 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(F)CCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 6, 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: [5, 1, 5, 14, 31, 103, 102, 103, 103, 103, 1, 1, 1, 1, 1, 1, 4, 4, 4, 17, 17, 17, 17, 17, 1, 15, 15, 103, 1, 1, 1, 1, 1, 4, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1] 201
rigid atoms, others: [32, 1, 43, 10, 11, 12, 13, 14, 15, 42, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 222
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497837 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(F)CCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 6, 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, 17, 38, 75, 114, 201, 201, 201, 201, 201, 17, 17, 17, 17, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 17, 75, 75, 201, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 201
rigid atoms, others: [34, 35, 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, 42, 43])
total number of confs: 502
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497837 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(F)CCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 15, 5, 5, 5, 5, 5, 7, 7, 6, 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: [73, 43, 13, 1, 1, 1, 1, 1, 1, 1, 73, 103, 103, 103, 103, 103, 149, 149, 149, 201, 201, 201, 201, 201, 103, 43, 43, 1, 103, 103, 103, 103, 103, 149, 201, 201, 201, 201, 201, 201, 201, 201, 103, 103] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 645
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497837 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497837
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497837/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497837
Building REAL300025497838
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497838'
/scratch/stefan/7787277/working/building/REAL300025497838 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497838

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497838/0 /scratch/stefan/7787277/working/building/REAL300025497838 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 712)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/712
`/scratch/stefan/7787277/working/3D/712' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497838.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497838.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497838/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497838 none CCC1=CC=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 14, 14, 14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 24, 76, 76, 76, 76, 76, 1, 20, 20, 20, 20, 20, 14, 14, 14, 5, 1, 1, 1, 1, 1, 13, 13, 76, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 44, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 196
number of broken/clashed sets: 56
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497838 none CCC1=CC=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 195, 195, 195, 195, 195, 195, 94, 94, 94, 76, 76, 76, 76, 76, 51, 29, 51, 12, 1, 1, 1, 1, 1, 1, 1, 76, 201, 201, 201, 201, 201, 195, 195, 195, 94, 76, 76, 76, 76, 76, 29, 29, 1, 76, 76] 201
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, 44, 45])
total number of confs: 469
number of broken/clashed sets: 56
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497838 none CCC1=CC=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 32, 32, 60, 100, 195, 195, 195, 195, 195, 14, 4, 4, 4, 4, 4, 1, 1, 1, 5, 14, 14, 14, 14, 14, 60, 60, 195, 14, 14] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 34, 33] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 460
number of broken/clashed sets: 56
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497838 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497838
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497838/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497838
Building REAL300025497839
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497839'
/scratch/stefan/7787277/working/building/REAL300025497839 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497839

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497839/0 /scratch/stefan/7787277/working/building/REAL300025497839 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 713)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/713
`/scratch/stefan/7787277/working/3D/713' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C(=O)NCC(F)F)C1)

`REAL300025497839.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497839.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497839/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497839 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C(=O)NCC(F)F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', '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, 1, 1, 5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 5, 7, 7, 6, 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, 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: [3, 1, 3, 9, 16, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 6, 23, 36, 36, 1, 9, 9, 67, 1, 1, 1, 1, 1, 5, 6, 23, 23, 36, 1, 1] 201
rigid atoms, others: [32, 1, 33, 40, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38])
total number of confs: 256
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: REAL300025497839 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C(=O)NCC(F)F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'F', 'F', '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, 1, 1, 5, 8, 1, 11, 1, 11, 8, 5, 5, 15, 15, 5, 7, 7, 6, 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, 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, 35, 13, 1, 1, 1, 1, 1, 1, 1, 51, 67, 67, 67, 67, 67, 100, 100, 100, 102, 102, 102, 201, 201, 201, 67, 35, 35, 1, 67, 67, 67, 67, 67, 100, 102, 201, 201, 201, 67, 67] 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: 821
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497839 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497839
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497839/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497839
Building REAL300025497840
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497840'
/scratch/stefan/7787277/working/building/REAL300025497840 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497840

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497840/0 /scratch/stefan/7787277/working/building/REAL300025497840 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 714)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/714
`/scratch/stefan/7787277/working/3D/714' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN(CCF)N=C2)C1)

`REAL300025497840.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497840.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497840/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497840 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN(CCF)N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 5, 5, 15, 8, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [5, 1, 5, 10, 17, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 33, 43, 9, 9, 1, 10, 10, 69, 1, 1, 1, 1, 1, 4, 9, 33, 33, 43, 43, 9, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 10, 11, 12, 13, 14, 15, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 282
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497840 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN(CCF)N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 5, 5, 15, 8, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [18, 9, 18, 26, 36, 119, 119, 119, 119, 119, 9, 9, 9, 9, 5, 5, 1, 5, 1, 1, 1, 1, 8, 13, 1, 1, 9, 26, 26, 119, 9, 9, 9, 9, 9, 5, 1, 8, 8, 13, 13, 1, 9, 9] 201
rigid atoms, others: [36, 41, 16, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 42, 43])
total number of confs: 270
number of broken/clashed sets: 63
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497840 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN(CCF)N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'F', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 5, 5, 15, 8, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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, 42, 13, 1, 1, 1, 1, 1, 1, 1, 59, 69, 69, 69, 69, 69, 71, 71, 71, 119, 119, 119, 201, 201, 119, 119, 69, 42, 42, 1, 69, 69, 69, 69, 69, 71, 119, 201, 201, 201, 201, 119, 69, 69] 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: 712
number of broken/clashed sets: 63
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497840 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497840
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497840/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497840
Building REAL300025497841
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497841'
/scratch/stefan/7787277/working/building/REAL300025497841 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497841

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497841/0 /scratch/stefan/7787277/working/building/REAL300025497841 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 715)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/715
`/scratch/stefan/7787277/working/3D/715' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497841.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497841.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497841/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497841 none CC1=CC(C)=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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: [15, 15, 15, 15, 15, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 50, 151, 151, 151, 151, 151, 1, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 26, 26, 151, 1, 1, 15] 201
rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45])
total number of confs: 298
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497841 none CC1=CC(C)=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 198, 198, 198, 151, 151, 151, 151, 151, 111, 44, 111, 13, 1, 1, 1, 1, 1, 1, 1, 151, 201, 201, 201, 201, 201, 201, 201, 201, 198, 151, 151, 151, 151, 151, 44, 44, 1, 151, 151, 201] 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: 605
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497841 none CC1=CC(C)=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 5, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 4, 4, 15, 15, 15, 15, 15, 36, 36, 85, 123, 201, 201, 201, 201, 201, 15, 1, 2, 2, 2, 1, 2, 2, 2, 4, 15, 15, 15, 15, 15, 85, 85, 201, 15, 15, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 45, 26, 30] set([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])
total number of confs: 527
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497841 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497841
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497841/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497841
Building REAL300025497842
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497842'
/scratch/stefan/7787277/working/building/REAL300025497842 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497842

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497842/0 /scratch/stefan/7787277/working/building/REAL300025497842 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 716)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/716
`/scratch/stefan/7787277/working/3D/716' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497842.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497842.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497842/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497842 none CN1C=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 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, 6, 7, 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: [14, 14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 39, 133, 133, 133, 133, 133, 1, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 16, 16, 133, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 239
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497842 none CN1C=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 186, 186, 186, 133, 133, 133, 133, 133, 108, 50, 108, 13, 1, 1, 1, 1, 1, 1, 1, 133, 201, 201, 201, 201, 201, 186, 133, 133, 133, 133, 133, 50, 50, 1, 133, 133] 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])
total number of confs: 622
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497842 none CN1C=NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 30, 30, 67, 114, 201, 201, 201, 201, 201, 14, 2, 2, 2, 1, 1, 6, 14, 14, 14, 14, 14, 67, 67, 201, 14, 14] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 482
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497842 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497842
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497842/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497842
Building REAL300025497843
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497843'
/scratch/stefan/7787277/working/building/REAL300025497843 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497843

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497843/0 /scratch/stefan/7787277/working/building/REAL300025497843 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 717)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/717
`/scratch/stefan/7787277/working/3D/717' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CC=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497843.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497843.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497843/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497843 none O=C(CCC1=CC=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens 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, 21, 24, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 13, 48, 48, 48, 48, 48, 1, 21, 21, 24, 24, 39, 39, 39, 39, 5, 1, 1, 1, 1, 1, 8, 8, 48, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 44, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 201
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497843 none O=C(CCC1=CC=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [75, 75, 75, 130, 147, 201, 201, 201, 201, 201, 48, 48, 48, 48, 48, 36, 25, 36, 13, 1, 1, 1, 1, 1, 1, 1, 48, 130, 130, 147, 147, 201, 201, 201, 201, 75, 48, 48, 48, 48, 48, 25, 25, 1, 48, 48] 201
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, 44, 45])
total number of confs: 699
number of broken/clashed sets: 61
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497843 none O=C(CCC1=CC=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens 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, 6, 2, 1, 1, 1, 1, 1, 1, 1, 22, 22, 39, 39, 39, 39, 39, 49, 49, 91, 130, 201, 201, 201, 201, 201, 39, 6, 6, 2, 2, 1, 1, 1, 1, 22, 39, 39, 39, 39, 39, 91, 91, 201, 39, 39] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 571
number of broken/clashed sets: 61
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497843 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497843
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497843/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497843
Building REAL300025497844
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497844'
/scratch/stefan/7787277/working/building/REAL300025497844 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497844

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497844/0 /scratch/stefan/7787277/working/building/REAL300025497844 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 718)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/718
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2=CNC3=CC=CC=C23)C1)

`REAL300025497844.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497844.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497844/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497844 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CNC3=CC=CC=C23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 23, 47, 134, 134, 134, 134, 134, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 18, 18, 18, 18, 18, 18, 1, 23, 23, 134, 1, 1, 1, 1, 1, 5, 18, 18, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 44, 10, 11, 12, 13, 14, 15, 43, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 264
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497844 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CNC3=CC=CC=C23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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, 7, 7, 7, 7]
0  hydrogens 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, 18, 47, 99, 137, 201, 201, 201, 201, 201, 18, 18, 18, 18, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 99, 99, 201, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [37, 38, 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, 43, 44])
total number of confs: 543
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497844 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CNC3=CC=CC=C23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [111, 44, 13, 1, 1, 1, 1, 1, 1, 1, 111, 134, 134, 134, 134, 134, 163, 163, 163, 201, 201, 201, 201, 201, 201, 201, 201, 134, 44, 44, 1, 134, 134, 134, 134, 134, 163, 201, 201, 201, 201, 201, 201, 134, 134] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 559
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497844 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497844
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497844/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497844
Building REAL300025497845
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497845'
/scratch/stefan/7787277/working/building/REAL300025497845 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497845

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497845/0 /scratch/stefan/7787277/working/building/REAL300025497845 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 719)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/719
`/scratch/stefan/7787277/working/3D/719' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)S1)

`REAL300025497845.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497845.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497845/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497845 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 14, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 35, 93, 93, 93, 93, 93, 1, 22, 22, 22, 22, 22, 22, 22, 5, 1, 1, 1, 1, 1, 19, 19, 93, 1, 1, 22, 22, 22] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43])
total number of confs: 213
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497845 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 14, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 118, 118, 118, 93, 93, 93, 93, 93, 77, 39, 77, 13, 1, 1, 1, 1, 1, 1, 1, 93, 201, 201, 201, 201, 201, 201, 201, 118, 93, 93, 93, 93, 93, 39, 39, 1, 93, 93, 201, 201, 201] 201
rigid atoms, others: [38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43])
total number of confs: 540
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497845 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 14, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 51, 51, 99, 138, 201, 201, 201, 201, 201, 22, 1, 1, 1, 2, 2, 2, 1, 7, 22, 22, 22, 22, 22, 99, 99, 201, 22, 22, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 582
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497845 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497845
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497845/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497845
Building REAL300025497846
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497846'
/scratch/stefan/7787277/working/building/REAL300025497846 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497846

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497846/0 /scratch/stefan/7787277/working/building/REAL300025497846 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 720)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/720
`/scratch/stefan/7787277/working/3D/720' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)NCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497846.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497846.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497846/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497846 none NC(=O)NCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 6, 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, 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, 108, 87, 83, 78, 41, 41, 41, 41, 41, 41, 41, 41, 35, 25, 35, 12, 1, 1, 1, 1, 1, 1, 1, 41, 109, 109, 109, 108, 108, 87, 87, 87, 87, 78, 78, 41, 41, 41, 41, 41, 41, 25, 25, 1, 41, 41] 109
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])
total number of confs: 487
number of broken/clashed sets: 90
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497846 none NC(=O)NCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [8, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [4, 7, 6, 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, 7]
0  hydrogens need rotated
109  conformations in input
total number of sets (complete confs): 109
using faster count positions algorithm for large data
unique positions, atoms: [26, 26, 26, 22, 11, 10, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 14, 41, 41, 41, 41, 41, 1, 26, 26, 26, 22, 22, 11, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 8, 8, 41, 1, 1] 109
rigid atoms, others: [48, 43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 197
number of broken/clashed sets: 90
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497846 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497846
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497846/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497846
Building REAL300025497847
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497847'
/scratch/stefan/7787277/working/building/REAL300025497847 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497847

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497847/0 /scratch/stefan/7787277/working/building/REAL300025497847 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 721)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/721
`/scratch/stefan/7787277/working/3D/721' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1)

`REAL300025497847.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497847.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497847/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497847 none CCC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 19, 33, 87, 87, 87, 87, 87, 1, 8, 15, 15, 15, 15, 15, 8, 8, 5, 1, 1, 1, 1, 1, 19, 19, 87, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 234
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497847 none CCC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 114, 114, 114, 114, 113, 113, 113, 87, 87, 87, 87, 87, 73, 37, 73, 13, 1, 1, 1, 1, 1, 1, 1, 87, 114, 201, 201, 201, 201, 201, 114, 114, 113, 87, 87, 87, 87, 87, 37, 37, 1, 87, 87] 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])
total number of confs: 888
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497847 none CCC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 17, 17, 39, 61, 114, 114, 114, 114, 114, 8, 1, 3, 3, 3, 3, 3, 1, 1, 4, 8, 8, 8, 8, 8, 39, 39, 114, 8, 8] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 283
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497847 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497847
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497847/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497847
Building REAL300025497848
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497848'
/scratch/stefan/7787277/working/building/REAL300025497848 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497848

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497848/0 /scratch/stefan/7787277/working/building/REAL300025497848 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 722)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/722
`/scratch/stefan/7787277/working/3D/722' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1)

`REAL300025497848.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497848.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497848/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497848 none CC1=CC=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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: [23, 23, 23, 23, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 25, 57, 57, 57, 57, 57, 1, 23, 23, 23, 23, 23, 23, 23, 17, 17, 5, 1, 1, 1, 1, 1, 15, 15, 57, 1, 1, 23, 23] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46])
total number of confs: 189
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497848 none CC1=CC=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 97, 97, 97, 57, 57, 57, 57, 57, 50, 31, 50, 13, 1, 1, 1, 1, 1, 1, 1, 57, 201, 201, 201, 201, 201, 201, 201, 201, 201, 97, 57, 57, 57, 57, 57, 31, 31, 1, 57, 57, 201, 201] 201
rigid atoms, others: [42, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46])
total number of confs: 793
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497848 none CC1=CC=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 8, 8, 8, 23, 23, 23, 23, 23, 50, 50, 86, 127, 201, 201, 201, 201, 201, 23, 1, 1, 2, 2, 2, 1, 1, 4, 4, 8, 23, 23, 23, 23, 23, 86, 86, 201, 23, 23, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 46, 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: 540
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497848 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497848
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497848/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497848
Building REAL300025497849
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497849'
/scratch/stefan/7787277/working/building/REAL300025497849 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497849

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497849/0 /scratch/stefan/7787277/working/building/REAL300025497849 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 723)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/723
`/scratch/stefan/7787277/working/3D/723' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SN=N1)

`REAL300025497849.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497849.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497849/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497849 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 28, 111, 111, 111, 111, 111, 1, 12, 12, 12, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 1, 14, 14, 111, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 257
number of broken/clashed sets: 46
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497849 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 182, 182, 146, 146, 146, 111, 111, 111, 111, 111, 69, 31, 69, 13, 1, 1, 1, 1, 1, 1, 1, 111, 182, 182, 182, 201, 201, 201, 201, 201, 146, 111, 111, 111, 111, 111, 31, 31, 1, 111, 111] 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])
total number of confs: 599
number of broken/clashed sets: 46
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497849 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 8, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 4, 4, 4, 12, 12, 12, 12, 12, 26, 26, 51, 83, 182, 182, 182, 182, 182, 12, 1, 1, 1, 3, 4, 4, 3, 3, 4, 12, 12, 12, 12, 12, 51, 51, 182, 12, 12] 201
rigid atoms, others: [1, 2, 3, 4, 23, 24, 25] set([0, 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: 410
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497849 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497849
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497849/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497849
Building REAL300025497850
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497850'
/scratch/stefan/7787277/working/building/REAL300025497850 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497850

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497850/0 /scratch/stefan/7787277/working/building/REAL300025497850 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 724)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/724
`/scratch/stefan/7787277/working/3D/724' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=CNC=CC3=N2)C1)

`REAL300025497850.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497850.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497850/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497850 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=CNC=CC3=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 32, 56, 148, 148, 148, 148, 148, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 1, 32, 32, 148, 1, 1, 1, 1, 1, 5, 10, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 304
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497850 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=CNC=CC3=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 10, 29, 82, 119, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 82, 82, 201, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 514
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497850 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=CNC=CC3=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [110, 44, 13, 1, 1, 1, 1, 1, 1, 1, 110, 148, 148, 148, 148, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 148, 44, 44, 1, 148, 148, 148, 148, 148, 201, 201, 201, 201, 201, 201, 148, 148] 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: 609
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497850 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497850
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497850/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497850
Building REAL300025497851
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497851'
/scratch/stefan/7787277/working/building/REAL300025497851 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497851

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497851/0 /scratch/stefan/7787277/working/building/REAL300025497851 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 725)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/725
`/scratch/stefan/7787277/working/3D/725' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)(C)C)

`REAL300025497851.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497851.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497851/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497851 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 11, 8, 5, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 148, 148, 148, 105, 105, 105, 105, 105, 88, 49, 88, 13, 1, 1, 1, 1, 1, 1, 1, 105, 201, 201, 201, 201, 201, 201, 201, 201, 148, 105, 105, 105, 105, 105, 49, 49, 1, 105, 105, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 806
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: REAL300025497851 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 11, 8, 5, 1, 1, 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, 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]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 32, 105, 105, 105, 105, 105, 1, 12, 13, 13, 13, 12, 12, 12, 12, 7, 1, 1, 1, 1, 1, 14, 14, 105, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 39, 20, 38, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 219
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497851 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497851
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497851/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497851
Building REAL300025497852
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497852'
/scratch/stefan/7787277/working/building/REAL300025497852 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497852

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497852/0 /scratch/stefan/7787277/working/building/REAL300025497852 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 726)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/726
`/scratch/stefan/7787277/working/3D/726' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CCC(CC2)C3)C1)

`REAL300025497852.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497852.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497852/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497852 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CCC(CC2)C3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens need 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, 25, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 1, 4, 4, 4, 16, 16, 16, 16, 16, 16, 1, 11, 11, 71, 1, 1, 1, 1, 1, 4, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 201
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 14, 15, 46, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 150
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497852 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CCC(CC2)C3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 16, 28, 66, 107, 201, 201, 201, 201, 201, 16, 16, 16, 16, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 16, 66, 66, 201, 16, 16, 16, 16, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 201
rigid atoms, others: [35, 36, 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, 46, 47])
total number of confs: 485
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497852 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CCC(CC2)C3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 33, 12, 1, 1, 1, 1, 1, 1, 1, 58, 71, 71, 71, 71, 71, 87, 87, 87, 201, 201, 201, 201, 201, 201, 71, 33, 33, 1, 71, 71, 71, 71, 71, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 71, 71] 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: 446
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497852 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497852
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497852/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497852
Building REAL300025497853
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497853'
/scratch/stefan/7787277/working/building/REAL300025497853 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025497853

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497853/0 /scratch/stefan/7787277/working/building/REAL300025497853 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 727)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/727
`/scratch/stefan/7787277/working/3D/727' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497853.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497853.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497853/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497853 none C[N@@H+]1CCCCC1C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
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, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 7, 7, 7, 7, 7, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 5, 5, 7, 1, 1] 8
rigid atoms, others: [48, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 29
number of broken/clashed sets: 1
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497853 none C[N@@H+]1CCCCC1C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
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, 7, 7, 7, 7, 7, 7, 6, 7, 5, 1, 1, 1, 1, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 6, 6, 1, 7, 7] 8
rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49])
total number of confs: 20
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497853 none C[N@@H+]1CCCCC1C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
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, 3, 3, 3, 4, 4, 4, 4, 4, 7, 7, 7, 7, 8, 8, 8, 8, 8, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 7, 7, 8, 4, 4] 8
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 32, 36, 33, 38, 37, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 29
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497853 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497853/1 /scratch/stefan/7787277/working/building/REAL300025497853 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 728)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/728
`/scratch/stefan/7787277/working/3D/728' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497853.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497853.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497853/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497853 none C[N@H+]1CCCCC1C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 6, 6, 6, 6, 6, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 1, 1, 1, 1, 1, 5, 5, 6, 1, 1] 11
rigid atoms, others: [48, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 27
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497853 none C[N@H+]1CCCCC1C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
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, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6] 11
rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49])
total number of confs: 37
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497853 none C[N@H+]1CCCCC1C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 9, 6, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
11  conformations in input
total number of sets (complete confs): 11
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 4, 7, 7, 9, 9, 11, 11, 11, 11, 11, 4, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 9, 9, 11, 4, 4] 11
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 32, 36, 33, 38, 37, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 43
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497853 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `2'
/scratch/stefan/7787277/working/building/REAL300025497853/2 /scratch/stefan/7787277/working/building/REAL300025497853 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 2 (index: 729)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/729
`/scratch/stefan/7787277/working/3D/729' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497853.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025497853.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497853/2/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: REAL300025497853 none CN1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 10, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 14, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 55, 148, 148, 148, 148, 148, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 6, 1, 1, 1, 1, 1, 27, 27, 148, 1, 1] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 309
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497853 none CN1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 10, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 201, 191, 191, 191, 148, 148, 148, 148, 148, 108, 43, 108, 13, 1, 1, 1, 1, 1, 1, 1, 148, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 191, 148, 148, 148, 148, 148, 43, 43, 1, 148, 148] 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: 603
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497853 none CN1CCCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 10, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 6, 6, 14, 14, 14, 14, 14, 34, 34, 90, 125, 201, 201, 201, 201, 201, 14, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 14, 14, 14, 14, 14, 90, 90, 201, 14, 14] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 37, 35, 36, 33, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 539
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497853 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497853
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497853/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497853/1.*
2: /scratch/stefan/7787277/working/building/REAL300025497853/2.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497853
Building REAL300025497854
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497854'
/scratch/stefan/7787277/working/building/REAL300025497854 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497854

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497854/0 /scratch/stefan/7787277/working/building/REAL300025497854 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 730)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/730
`/scratch/stefan/7787277/working/3D/730' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1Cl)

`REAL300025497854.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497854.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497854/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497854 none CN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 16, 7, 7, 7, 7, 6, 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, 6, 7, 7, 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: [14, 14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 30, 91, 91, 91, 91, 91, 1, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 15, 15, 91, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 40, 23, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 188
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497854 none CN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 16, 7, 7, 7, 7, 6, 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, 6, 7, 7, 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, 111, 111, 111, 91, 91, 91, 91, 91, 74, 45, 74, 13, 1, 1, 1, 1, 1, 1, 1, 91, 201, 201, 201, 201, 201, 201, 111, 91, 91, 91, 91, 91, 45, 45, 1, 91, 91] 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])
total number of confs: 508
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497854 none CN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 16, 7, 7, 7, 7, 6, 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, 6, 7, 7, 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, 5, 5, 5, 14, 14, 14, 14, 14, 36, 36, 65, 107, 201, 201, 201, 201, 201, 14, 1, 1, 2, 2, 2, 1, 5, 14, 14, 14, 14, 14, 65, 65, 201, 14, 14] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 485
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497854 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497854
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497854/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497854
Building REAL300025497855
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497855'
/scratch/stefan/7787277/working/building/REAL300025497855 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497855

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497855/0 /scratch/stefan/7787277/working/building/REAL300025497855 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 731)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/731
`/scratch/stefan/7787277/working/3D/731' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=C(F)C=C2F)C1)

`REAL300025497855.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497855.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497855/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497855 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=C(F)C=C2F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 1, 15, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 20, 43, 149, 149, 149, 149, 149, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 1, 20, 20, 149, 1, 1, 1, 1, 1, 4, 11, 11, 1, 1] 201
rigid atoms, others: [32, 1, 34, 38, 33, 10, 11, 12, 13, 14, 15, 39, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37])
total number of confs: 268
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497855 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=C(F)C=C2F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 1, 15, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 11, 31, 73, 118, 201, 201, 201, 201, 201, 11, 11, 11, 11, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 11, 73, 73, 201, 11, 11, 11, 11, 11, 7, 1, 1, 11, 11] 201
rigid atoms, others: [36, 37, 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, 38, 39])
total number of confs: 487
number of broken/clashed sets: 31
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497855 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=C(F)C=C2F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 1, 1, 15, 1, 1, 15, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [110, 47, 13, 1, 1, 1, 1, 1, 1, 1, 110, 149, 149, 149, 149, 149, 197, 197, 197, 201, 201, 201, 201, 201, 201, 201, 149, 47, 47, 1, 149, 149, 149, 149, 149, 197, 201, 201, 149, 149] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 598
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497855 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497855
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497855/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497855
Building REAL300025497856
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497856'
/scratch/stefan/7787277/working/building/REAL300025497856 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497856

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497856/0 /scratch/stefan/7787277/working/building/REAL300025497856 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 732)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/732
`/scratch/stefan/7787277/working/3D/732' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)S(C)(=O)=O)

`REAL300025497856.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497856.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497856/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497856 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)S(C)(=O)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 6, 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, 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, 131, 131, 131, 86, 86, 86, 86, 86, 78, 57, 78, 13, 1, 1, 1, 1, 1, 1, 1, 86, 201, 201, 201, 201, 201, 201, 201, 201, 131, 86, 86, 86, 86, 86, 57, 57, 1, 86, 86, 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])
total number of confs: 826
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: REAL300025497856 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)S(C)(=O)=O NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 5, 11, 11, 7, 7, 7, 7, 6, 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, 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: [20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 12, 19, 86, 86, 86, 86, 86, 1, 20, 26, 26, 26, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 12, 12, 86, 1, 1, 26, 26, 26] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 39, 20, 38, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42])
total number of confs: 235
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497856 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497856
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497856/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497856
Building REAL300025497857
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497857'
/scratch/stefan/7787277/working/building/REAL300025497857 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497857

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497857/0 /scratch/stefan/7787277/working/building/REAL300025497857 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 733)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/733
`/scratch/stefan/7787277/working/3D/733' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CS(=O)(=O)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497857.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497857.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497857/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497857 none CS(=O)(=O)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 14, 11, 11, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 3, 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]
0  hydrogens need rotated
201  conformations 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, 123, 123, 123, 98, 98, 98, 98, 98, 58, 28, 58, 13, 1, 1, 1, 1, 1, 1, 1, 98, 201, 201, 201, 201, 201, 196, 196, 123, 98, 98, 98, 98, 98, 28, 28, 1, 98, 98] 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])
total number of confs: 733
number of broken/clashed sets: 73
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497857 none CS(=O)(=O)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'S.o2', 'O.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 14, 11, 11, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 3, 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]
0  hydrogens 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, 21, 28, 28, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 28, 98, 98, 98, 98, 98, 1, 28, 28, 28, 21, 21, 18, 18, 4, 1, 1, 1, 1, 1, 15, 15, 98, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 281
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497857 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497857
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497857/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497857
Building REAL300025497858
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497858'
/scratch/stefan/7787277/working/building/REAL300025497858 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497858

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497858/0 /scratch/stefan/7787277/working/building/REAL300025497858 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 734)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/734
`/scratch/stefan/7787277/working/3D/734' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CC=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497858.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497858.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497858/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497858 none O=C(CC1=CC=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 16, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 21, 47, 47, 47, 47, 47, 1, 16, 16, 30, 30, 30, 30, 5, 1, 1, 1, 1, 1, 14, 14, 47, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 182
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497858 none O=C(CC1=CC=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [61, 61, 61, 132, 201, 201, 201, 201, 201, 47, 47, 47, 47, 47, 45, 32, 45, 13, 1, 1, 1, 1, 1, 1, 1, 47, 132, 132, 201, 201, 201, 201, 61, 47, 47, 47, 47, 47, 32, 32, 1, 47, 47] 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])
total number of confs: 672
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497858 none O=C(CC1=CC=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 1, 11, 11, 30, 30, 30, 30, 30, 57, 57, 99, 132, 201, 201, 201, 201, 201, 30, 4, 4, 1, 1, 1, 1, 11, 30, 30, 30, 30, 30, 99, 99, 201, 30, 30] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 561
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497858 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497858
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497858/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497858
Building REAL300025497859
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497859'
/scratch/stefan/7787277/working/building/REAL300025497859 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497859

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497859/0 /scratch/stefan/7787277/working/building/REAL300025497859 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 735)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/735
`/scratch/stefan/7787277/working/3D/735' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1)

`REAL300025497859.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497859.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497859/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497859 none CCC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 36, 104, 104, 104, 104, 104, 1, 5, 17, 17, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 19, 19, 104, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 255
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497859 none CCC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 128, 128, 128, 128, 128, 128, 128, 104, 104, 104, 104, 104, 84, 41, 84, 13, 1, 1, 1, 1, 1, 1, 1, 104, 128, 201, 201, 201, 201, 201, 128, 128, 128, 104, 104, 104, 104, 104, 41, 41, 1, 104, 104] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43])
total number of confs: 844
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497859 none CCC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 15, 15, 38, 61, 128, 128, 128, 128, 128, 5, 1, 7, 7, 7, 6, 6, 1, 1, 1, 5, 5, 5, 5, 5, 38, 38, 128, 5, 5] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 9, 25, 33, 31] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 320
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497859 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497859
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497859/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497859
Building REAL300025497860
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497860'
/scratch/stefan/7787277/working/building/REAL300025497860 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497860

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497860/0 /scratch/stefan/7787277/working/building/REAL300025497860 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 736)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/736
`/scratch/stefan/7787277/working/3D/736' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1=O)

`REAL300025497860.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497860.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497860/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497860 none CN1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 32, 80, 80, 80, 80, 80, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 1, 18, 18, 80, 1, 1, 23, 23] 201
rigid atoms, others: [45, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 40, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47])
total number of confs: 220
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497860 none CN1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 106, 106, 106, 80, 80, 80, 80, 80, 63, 38, 63, 13, 1, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 80, 80, 80, 80, 80, 38, 38, 1, 80, 80, 201, 201] 201
rigid atoms, others: [43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47])
total number of confs: 631
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497860 none CN1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 23, 23, 23, 23, 23, 51, 51, 97, 139, 201, 201, 201, 201, 201, 23, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 8, 23, 23, 23, 23, 23, 97, 97, 201, 23, 23, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 46, 47, 24, 25, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 557
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497860 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497860
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497860/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497860
Building REAL300025497861
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497861'
/scratch/stefan/7787277/working/building/REAL300025497861 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497861

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497861/0 /scratch/stefan/7787277/working/building/REAL300025497861 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 737)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/737
`/scratch/stefan/7787277/working/3D/737' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC1=O)

`REAL300025497861.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497861.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497861/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497861 none CN1C=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 27, 88, 88, 88, 88, 88, 1, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 15, 15, 88, 1, 1, 13] 201
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 180
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497861 none CN1C=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 101, 101, 101, 88, 88, 88, 88, 88, 67, 44, 67, 12, 1, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 201, 201, 201, 201, 201, 101, 88, 88, 88, 88, 88, 44, 44, 1, 88, 88, 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])
total number of confs: 479
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497861 none CN1C=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 11, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 13, 13, 13, 13, 13, 31, 31, 69, 107, 201, 201, 201, 201, 201, 13, 1, 1, 1, 2, 2, 2, 1, 1, 5, 13, 13, 13, 13, 13, 69, 69, 201, 13, 13, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 502
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497861 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497861
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497861/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497861
Building REAL300025497862
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497862'
/scratch/stefan/7787277/working/building/REAL300025497862 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497862

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497862/0 /scratch/stefan/7787277/working/building/REAL300025497862 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 738)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/738
`/scratch/stefan/7787277/working/3D/738' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(F)(F)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497862.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497862.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497862/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497862 none CC(F)(F)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 15, 15, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 184, 108, 108, 108, 74, 74, 74, 74, 74, 56, 30, 56, 13, 1, 1, 1, 1, 1, 1, 1, 74, 201, 201, 201, 201, 201, 184, 184, 108, 74, 74, 74, 74, 74, 30, 30, 1, 74, 74] 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])
total number of confs: 798
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497862 none CC(F)(F)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 15, 15, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [34, 32, 34, 34, 24, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 74, 74, 74, 74, 74, 1, 34, 34, 34, 32, 32, 24, 24, 5, 1, 1, 1, 1, 1, 9, 9, 74, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 251
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497862 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497862
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497862/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497862
Building REAL300025497863
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497863'
/scratch/stefan/7787277/working/building/REAL300025497863 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497863

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497863/0 /scratch/stefan/7787277/working/building/REAL300025497863 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 739)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/739
`/scratch/stefan/7787277/working/3D/739' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COC1CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497863.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497863.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497863/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497863 none O=C(COC1CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 3, 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]
0  hydrogens 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, 24, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 11, 55, 55, 55, 55, 55, 1, 10, 10, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 1, 1, 1, 1, 1, 5, 5, 55, 1, 1] 201
rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48])
total number of confs: 177
number of broken/clashed sets: 79
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497863 none O=C(COC1CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 3, 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]
0  hydrogens 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, 144, 160, 201, 201, 201, 201, 201, 55, 55, 55, 55, 55, 45, 30, 45, 13, 1, 1, 1, 1, 1, 1, 1, 55, 144, 144, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 83, 55, 55, 55, 55, 55, 30, 30, 1, 55, 55] 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, 50])
total number of confs: 768
number of broken/clashed sets: 79
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497863 none O=C(COC1CCCCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 12, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 3, 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]
0  hydrogens 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, 5, 1, 1, 1, 1, 1, 1, 1, 23, 23, 36, 36, 36, 36, 36, 48, 48, 85, 125, 201, 201, 201, 201, 201, 36, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 36, 36, 36, 36, 36, 85, 85, 201, 36, 36] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 39, 37, 35, 36, 38, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 542
number of broken/clashed sets: 79
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497863 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497863
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497863/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497863
Building REAL300025497864
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497864'
/scratch/stefan/7787277/working/building/REAL300025497864 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497864

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497864/0 /scratch/stefan/7787277/working/building/REAL300025497864 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 740)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/740
`/scratch/stefan/7787277/working/3D/740' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CC=NC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497864.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497864.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497864/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497864 none O=C(CCC1=CC=NC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens 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, 24, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 72, 72, 72, 72, 72, 1, 24, 24, 28, 28, 28, 28, 28, 28, 5, 1, 1, 1, 1, 1, 13, 13, 72, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 44, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 228
number of broken/clashed sets: 44
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497864 none O=C(CCC1=CC=NC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [90, 90, 90, 176, 201, 201, 201, 201, 201, 201, 72, 72, 72, 72, 72, 43, 28, 43, 13, 1, 1, 1, 1, 1, 1, 1, 72, 176, 176, 201, 201, 201, 201, 201, 201, 90, 72, 72, 72, 72, 72, 28, 28, 1, 72, 72] 201
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, 44, 45])
total number of confs: 792
number of broken/clashed sets: 44
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497864 none O=C(CCC1=CC=NC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 8, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 28, 28, 28, 28, 28, 55, 55, 95, 132, 201, 201, 201, 201, 201, 28, 3, 3, 1, 1, 1, 1, 1, 1, 12, 28, 28, 28, 28, 28, 95, 95, 201, 28, 28] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 570
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497864 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497864
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497864/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497864
Building REAL300025497865
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497865'
/scratch/stefan/7787277/working/building/REAL300025497865 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497865

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497865/0 /scratch/stefan/7787277/working/building/REAL300025497865 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 741)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/741
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2CCC(=O)NC2)C1)

`REAL300025497865.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497865.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497865/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497865 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC(=O)NC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 14, 29, 90, 90, 90, 90, 90, 1, 1, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 1, 14, 14, 90, 1, 1, 1, 1, 1, 4, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1] 201
rigid atoms, others: [32, 1, 43, 33, 44, 10, 11, 12, 13, 14, 15, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 193
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497865 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC(=O)NC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 15, 43, 82, 119, 201, 201, 201, 201, 201, 15, 15, 15, 15, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 15, 82, 82, 201, 15, 15, 15, 15, 15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 201
rigid atoms, others: [35, 36, 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, 43, 44])
total number of confs: 517
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497865 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC(=O)NC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [67, 41, 13, 1, 1, 1, 1, 1, 1, 1, 67, 90, 90, 90, 90, 90, 124, 124, 124, 201, 201, 201, 201, 201, 201, 90, 41, 41, 1, 90, 90, 90, 90, 90, 124, 201, 201, 201, 201, 201, 201, 201, 201, 90, 90] 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: 654
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497865 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497865
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497865/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497865
Building REAL300025497866
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497866'
/scratch/stefan/7787277/working/building/REAL300025497866 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497866

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497866/0 /scratch/stefan/7787277/working/building/REAL300025497866 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 742)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/742
`/scratch/stefan/7787277/working/3D/742' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC=N1)

`REAL300025497866.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497866.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497866/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497866 none COC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 32, 71, 71, 71, 71, 71, 1, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 19, 19, 71, 1, 1, 17, 17] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43])
total number of confs: 180
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497866 none COC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 86, 86, 86, 71, 71, 71, 71, 71, 56, 37, 56, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 201, 201, 86, 71, 71, 71, 71, 71, 37, 37, 1, 71, 71, 201, 201] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 453
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497866 none COC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 51, 51, 95, 136, 201, 201, 201, 201, 201, 17, 1, 1, 1, 2, 2, 2, 1, 5, 17, 17, 17, 17, 17, 95, 95, 201, 17, 17, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 43, 24, 25, 26, 30] set([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])
total number of confs: 549
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497866 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497866
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497866/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497866
Building REAL300025497867
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497867'
/scratch/stefan/7787277/working/building/REAL300025497867 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497867

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497867/0 /scratch/stefan/7787277/working/building/REAL300025497867 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 743)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/743
`/scratch/stefan/7787277/working/3D/743' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC1=NNC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497867.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497867.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497867/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497867 none CCCC1=NNC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens 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, 33, 13, 13, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 64, 64, 64, 64, 64, 1, 38, 38, 38, 38, 38, 33, 33, 13, 13, 5, 1, 1, 1, 1, 1, 6, 6, 64, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 235
number of broken/clashed sets: 56
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497867 none CCCC1=NNC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 165, 165, 165, 165, 165, 118, 118, 118, 64, 64, 64, 64, 64, 53, 30, 53, 13, 1, 1, 1, 1, 1, 1, 1, 64, 201, 201, 201, 201, 201, 201, 201, 165, 165, 118, 64, 64, 64, 64, 64, 30, 30, 1, 64, 64] 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])
total number of confs: 677
number of broken/clashed sets: 56
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497867 none CCCC1=NNC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens 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, 1, 4, 4, 4, 13, 13, 13, 13, 13, 22, 22, 41, 66, 165, 165, 165, 165, 165, 13, 9, 9, 9, 8, 8, 5, 5, 1, 1, 4, 13, 13, 13, 13, 13, 41, 41, 165, 13, 13] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 34, 35] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 377
number of broken/clashed sets: 56
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497867 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497867
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497867/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497867
Building REAL300025497868
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497868'
/scratch/stefan/7787277/working/building/REAL300025497868 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497868

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497868/0 /scratch/stefan/7787277/working/building/REAL300025497868 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 744)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/744
`/scratch/stefan/7787277/working/3D/744' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NNC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497868.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497868.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497868/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497868 none CCC1=NNC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 12, 12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 26, 105, 105, 105, 105, 105, 1, 26, 26, 26, 26, 26, 12, 12, 5, 1, 1, 1, 1, 1, 14, 14, 105, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 263
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497868 none CCC1=NNC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 160, 160, 160, 160, 160, 142, 142, 142, 105, 105, 105, 105, 105, 70, 31, 70, 13, 1, 1, 1, 1, 1, 1, 1, 105, 201, 201, 201, 201, 201, 160, 160, 142, 105, 105, 105, 105, 105, 31, 31, 1, 105, 105] 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])
total number of confs: 688
number of broken/clashed sets: 59
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497868 none CCC1=NNC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 12, 12, 12, 12, 12, 26, 26, 54, 86, 160, 160, 160, 160, 160, 12, 3, 3, 3, 3, 3, 1, 1, 4, 12, 12, 12, 12, 12, 54, 54, 160, 12, 12] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 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, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 393
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497868 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497868
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497868/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497868
Building REAL300025497869
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497869'
/scratch/stefan/7787277/working/building/REAL300025497869 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497869

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497869/0 /scratch/stefan/7787277/working/building/REAL300025497869 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 745)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/745
`/scratch/stefan/7787277/working/3D/745' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=NNC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497869.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497869.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497869/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497869 none CC(C)C1=NNC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens 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, 17, 19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 29, 100, 100, 100, 100, 100, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 5, 1, 1, 1, 1, 1, 15, 15, 100, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 207
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497869 none CC(C)C1=NNC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in 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, 201, 140, 140, 140, 100, 100, 100, 100, 100, 60, 29, 60, 12, 1, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 201, 201, 201, 201, 201, 140, 100, 100, 100, 100, 100, 29, 29, 1, 100, 100] 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])
total number of confs: 585
number of broken/clashed sets: 36
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497869 none CC(C)C1=NNC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 19, 19, 19, 19, 19, 49, 49, 92, 130, 201, 201, 201, 201, 201, 19, 2, 2, 2, 1, 2, 2, 2, 1, 1, 7, 19, 19, 19, 19, 19, 92, 92, 201, 19, 19] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 541
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497869 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497869
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497869/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497869
Building REAL300025497870
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497870'
/scratch/stefan/7787277/working/building/REAL300025497870 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497870

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497870/0 /scratch/stefan/7787277/working/building/REAL300025497870 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 746)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/746
`/scratch/stefan/7787277/working/3D/746' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NNC3=C2CCC3)C1)

`REAL300025497870.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497870.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497870/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497870 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NNC3=C2CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 47, 147, 147, 147, 147, 147, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 1, 20, 20, 147, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 8, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 44, 10, 11, 12, 13, 14, 15, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 263
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497870 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NNC3=C2CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 28, 62, 104, 201, 201, 201, 201, 201, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 8, 62, 62, 201, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 16, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44])
total number of confs: 453
number of broken/clashed sets: 29
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497870 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NNC3=C2CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 1, 1, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 43, 13, 1, 1, 1, 1, 1, 1, 1, 109, 147, 147, 147, 147, 147, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 43, 43, 1, 147, 147, 147, 147, 147, 201, 201, 201, 201, 201, 201, 201, 201, 147, 147] 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: 607
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497870 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497870/1 /scratch/stefan/7787277/working/building/REAL300025497870 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 747)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/747
`/scratch/stefan/7787277/working/3D/747' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3CCCC3=NN2)C1)

`REAL300025497870.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497870.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497870/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497870 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3CCCC3=NN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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: [6, 1, 6, 20, 41, 127, 127, 127, 127, 127, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 12, 12, 1, 20, 20, 127, 1, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 12, 12, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 44, 10, 11, 12, 13, 14, 15, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 244
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497870 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3CCCC3=NN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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, 12, 33, 70, 104, 201, 201, 201, 201, 201, 12, 12, 12, 12, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 12, 70, 70, 201, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 1, 1, 12, 12] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 16, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44])
total number of confs: 472
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497870 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3CCCC3=NN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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: [95, 40, 13, 1, 1, 1, 1, 1, 1, 1, 95, 127, 127, 127, 127, 127, 194, 194, 194, 201, 201, 201, 201, 201, 201, 201, 127, 40, 40, 1, 127, 127, 127, 127, 127, 194, 201, 201, 201, 201, 201, 201, 201, 127, 127] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 609
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497870 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497870
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497870/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497870/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497870
Building REAL300025497871
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497871'
/scratch/stefan/7787277/working/building/REAL300025497871 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497871

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497871/0 /scratch/stefan/7787277/working/building/REAL300025497871 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 748)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/748
`/scratch/stefan/7787277/working/3D/748' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NNN=C2)C1)

`REAL300025497871.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497871.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497871/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497871 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NNN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 21, 49, 137, 137, 137, 137, 137, 1, 1, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 1, 21, 21, 137, 1, 1, 1, 1, 1, 6, 7, 8, 1, 1] 201
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34])
total number of confs: 256
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497871 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NNN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 8, 23, 57, 100, 201, 201, 201, 201, 201, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 57, 57, 201, 8, 8, 8, 8, 8, 3, 1, 1, 8, 8] 201
rigid atoms, others: [33, 34, 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, 35, 36])
total number of confs: 438
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497871 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NNN=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 8, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [104, 42, 13, 1, 1, 1, 1, 1, 1, 1, 104, 137, 137, 137, 137, 137, 201, 201, 201, 201, 201, 201, 201, 137, 42, 42, 1, 137, 137, 137, 137, 137, 201, 201, 201, 137, 137] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 630
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497871 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497871/1 /scratch/stefan/7787277/working/building/REAL300025497871 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 749)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/749
`/scratch/stefan/7787277/working/3D/749' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=NN2)C1)

`REAL300025497871.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497871.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497871/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497871 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=NN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 20, 40, 117, 117, 117, 117, 117, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 1, 20, 20, 117, 1, 1, 1, 1, 1, 5, 10, 10, 1, 1] 201
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34])
total number of confs: 234
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497871 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=NN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 29, 67, 101, 201, 201, 201, 201, 201, 10, 10, 10, 10, 3, 3, 1, 3, 1, 1, 1, 1, 1, 10, 67, 67, 201, 10, 10, 10, 10, 10, 3, 1, 1, 10, 10] 201
rigid atoms, others: [33, 34, 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, 35, 36])
total number of confs: 462
number of broken/clashed sets: 28
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497871 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=NN2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 8, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [87, 40, 13, 1, 1, 1, 1, 1, 1, 1, 87, 117, 117, 117, 117, 117, 183, 183, 183, 201, 201, 201, 201, 117, 40, 40, 1, 117, 117, 117, 117, 117, 183, 201, 201, 117, 117] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 629
number of broken/clashed sets: 28
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497871 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497871
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497871/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497871/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497871
Building REAL300025497872
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497872'
/scratch/stefan/7787277/working/building/REAL300025497872 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497872

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497872/0 /scratch/stefan/7787277/working/building/REAL300025497872 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 750)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/750
`/scratch/stefan/7787277/working/3D/750' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1CCCCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497872.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497872.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497872/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497872 none O=C(CN1CCCCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 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: [4, 4, 4, 20, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 27, 101, 101, 101, 101, 101, 1, 20, 20, 24, 24, 24, 24, 24, 24, 24, 24, 4, 1, 1, 1, 1, 1, 16, 16, 101, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 241
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497872 none O=C(CN1CCCCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 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: [126, 126, 126, 200, 201, 201, 201, 201, 201, 201, 101, 101, 101, 101, 101, 55, 29, 55, 13, 1, 1, 1, 1, 1, 1, 1, 101, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 126, 101, 101, 101, 101, 101, 29, 29, 1, 101, 101] 201
rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47])
total number of confs: 728
number of broken/clashed sets: 50
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497872 none O=C(CN1CCCCC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 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: [14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 24, 24, 24, 24, 24, 49, 49, 82, 124, 201, 201, 201, 201, 201, 24, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 14, 24, 24, 24, 24, 24, 82, 82, 201, 24, 24] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 522
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497872 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497872
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497872/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497872
Building REAL300025497873
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497873'
/scratch/stefan/7787277/working/building/REAL300025497873 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497873

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497873/0 /scratch/stefan/7787277/working/building/REAL300025497873 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 751)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/751
`/scratch/stefan/7787277/working/3D/751' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CC1=O)

`REAL300025497873.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497873.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497873/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497873 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 6, 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, 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: [14, 14, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 28, 80, 80, 80, 80, 80, 1, 14, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 15, 15, 80, 1, 1, 14, 14] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43])
total number of confs: 171
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497873 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 6, 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, 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, 93, 93, 93, 80, 80, 80, 80, 80, 60, 41, 60, 11, 1, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 201, 201, 201, 201, 201, 93, 80, 80, 80, 80, 80, 41, 41, 1, 80, 80, 201, 201] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 459
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497873 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 6, 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, 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, 5, 5, 5, 14, 14, 14, 14, 14, 37, 37, 78, 115, 201, 201, 201, 201, 201, 14, 1, 1, 1, 1, 2, 2, 2, 1, 5, 14, 14, 14, 14, 14, 78, 78, 201, 14, 14, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 42, 43, 23, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 516
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497873 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497873
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497873/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497873
Building REAL300025497874
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497874'
/scratch/stefan/7787277/working/building/REAL300025497874 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497874

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497874/0 /scratch/stefan/7787277/working/building/REAL300025497874 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 752)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/752
`/scratch/stefan/7787277/working/3D/752' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C)

`REAL300025497874.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497874.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497874/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497874 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 24, 67, 67, 67, 67, 67, 1, 20, 20, 20, 20, 33, 33, 33, 33, 33, 4, 1, 1, 1, 1, 1, 14, 14, 67, 1, 1, 20, 20, 20, 20] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46])
total number of confs: 231
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497874 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 153, 153, 101, 101, 101, 67, 67, 67, 67, 67, 52, 26, 52, 13, 1, 1, 1, 1, 1, 1, 1, 67, 153, 153, 153, 153, 201, 201, 201, 201, 201, 101, 67, 67, 67, 67, 67, 26, 26, 1, 67, 67, 153, 153, 153, 153] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46])
total number of confs: 688
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497874 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 8, 8, 8, 20, 20, 20, 20, 20, 35, 35, 59, 88, 153, 153, 153, 153, 153, 20, 1, 1, 1, 1, 3, 3, 3, 3, 3, 8, 20, 20, 20, 20, 20, 59, 59, 153, 20, 20, 1, 2, 2, 2] 201
rigid atoms, others: [1, 2, 3, 4, 43, 23, 24, 25, 26] set([0, 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: 406
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497874 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497874
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497874/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497874
Building REAL300025497875
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497875'
/scratch/stefan/7787277/working/building/REAL300025497875 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497875

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497875/0 /scratch/stefan/7787277/working/building/REAL300025497875 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 753)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/753
`/scratch/stefan/7787277/working/3D/753' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1CCCNC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497875.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497875.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497875/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497875 none O=C(CN1CCCNC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 8, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens 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, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 29, 96, 96, 96, 96, 96, 1, 21, 21, 27, 27, 27, 27, 27, 27, 27, 4, 1, 1, 1, 1, 1, 16, 16, 96, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 249
number of broken/clashed sets: 57
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497875 none O=C(CN1CCCNC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 8, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens 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, 201, 96, 96, 96, 96, 96, 54, 28, 54, 13, 1, 1, 1, 1, 1, 1, 1, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201, 116, 96, 96, 96, 96, 96, 28, 28, 1, 96, 96] 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])
total number of confs: 749
number of broken/clashed sets: 57
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497875 none O=C(CN1CCCNC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 5, 5, 5, 8, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens 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, 1, 16, 16, 27, 27, 27, 27, 27, 53, 53, 83, 126, 201, 201, 201, 201, 201, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 16, 27, 27, 27, 27, 27, 83, 83, 201, 27, 27] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 524
number of broken/clashed sets: 57
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497875 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497875
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497875/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497875
Building REAL300025497876
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497876'
/scratch/stefan/7787277/working/building/REAL300025497876 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497876

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497876/0 /scratch/stefan/7787277/working/building/REAL300025497876 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 754)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/754
`/scratch/stefan/7787277/working/3D/754' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)C(C)(C)C1(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497876.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497876.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497876/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497876 none CC1(C)C(C)(C)C1(C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens 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, 5, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 39, 121, 121, 121, 121, 121, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 18, 18, 121, 1, 1] 201
rigid atoms, others: [11, 47, 44, 10, 43, 12, 13, 14, 45, 16, 51, 52, 46, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 234
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497876 none CC1(C)C(C)(C)C1(C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 152, 201, 152, 152, 121, 121, 121, 121, 121, 100, 52, 100, 13, 1, 1, 1, 1, 1, 1, 1, 121, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 121, 121, 121, 121, 121, 52, 52, 1, 121, 121] 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: 674
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497876 none CC1(C)C(C)(C)C1(C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 33, 33, 60, 110, 201, 201, 201, 201, 201, 9, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 9, 9, 9, 9, 9, 60, 60, 201, 9, 9] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 480
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497876 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497876
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497876/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497876
Building REAL300025497877
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497877'
/scratch/stefan/7787277/working/building/REAL300025497877 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497877

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497877/0 /scratch/stefan/7787277/working/building/REAL300025497877 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 755)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/755
`/scratch/stefan/7787277/working/3D/755' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1)

`REAL300025497877.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497877.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497877/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497877 none C=CCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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]
0  hydrogens 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, 7, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 76, 76, 76, 76, 76, 1, 7, 7, 7, 7, 21, 21, 21, 16, 16, 4, 1, 1, 1, 1, 1, 11, 11, 76, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 213
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497877 none C=CCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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]
0  hydrogens need rotated
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, 131, 131, 131, 76, 76, 76, 76, 76, 59, 27, 59, 13, 1, 1, 1, 1, 1, 1, 1, 76, 191, 191, 191, 191, 201, 201, 201, 201, 201, 131, 76, 76, 76, 76, 76, 27, 27, 1, 76, 76, 191, 191, 191, 191, 191, 191, 191, 191] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 685
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497877 none C=CCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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: [1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 7, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 15, 15, 44, 80, 191, 191, 191, 191, 191, 7, 1, 1, 1, 1, 10, 10, 10, 7, 7, 3, 7, 7, 7, 7, 7, 44, 44, 191, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 3, 4, 43, 44, 45, 46, 47, 48, 49, 50, 23, 24, 25, 26] set([0, 1, 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: 430
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497877 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497877
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497877/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497877
Building REAL300025497878
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497878'
/scratch/stefan/7787277/working/building/REAL300025497878 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497878

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497878/0 /scratch/stefan/7787277/working/building/REAL300025497878 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 756)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/756
`/scratch/stefan/7787277/working/3D/756' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)NC=N1)

`REAL300025497878.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497878.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497878/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497878 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 27, 78, 78, 78, 78, 78, 1, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 12, 12, 78, 1, 1, 16, 16] 201
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 37, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40])
total number of confs: 161
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497878 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 99, 99, 99, 78, 78, 78, 78, 78, 66, 38, 66, 13, 1, 1, 1, 1, 1, 1, 1, 78, 201, 201, 201, 201, 201, 201, 99, 78, 78, 78, 78, 78, 38, 38, 1, 78, 78, 201, 201] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40])
total number of confs: 481
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497878 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 16, 16, 16, 16, 16, 32, 32, 61, 97, 201, 201, 201, 201, 201, 16, 1, 1, 1, 2, 2, 2, 7, 16, 16, 16, 16, 16, 61, 61, 201, 16, 16, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 39, 40, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 484
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497878 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497878
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497878/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497878
Building REAL300025497879
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497879'
/scratch/stefan/7787277/working/building/REAL300025497879 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497879

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497879/0 /scratch/stefan/7787277/working/building/REAL300025497879 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 757)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/757
`/scratch/stefan/7787277/working/3D/757' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1CCOCC1)

`REAL300025497879.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497879.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497879/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497879 none C[C@@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 201, 161, 161, 117, 117, 117, 117, 117, 70, 31, 70, 13, 1, 1, 1, 1, 1, 1, 1, 117, 201, 201, 201, 201, 201, 201, 201, 201, 201, 161, 117, 117, 117, 117, 117, 31, 31, 1, 117, 117, 201, 201, 201, 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, 48, 49])
total number of confs: 657
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497879 none C[C@@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 6, 7, 7, 7, 18, 18, 18, 18, 18, 43, 43, 79, 115, 201, 201, 201, 201, 201, 18, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 18, 18, 18, 18, 18, 79, 79, 201, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 42, 43, 44, 45, 46, 47, 48, 49, 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])
total number of confs: 508
number of broken/clashed sets: 53
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497879 none C[C@@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)N1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 10, 5, 5, 12, 5, 5, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 33, 117, 117, 117, 117, 117, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 17, 17, 117, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 41] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 255
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497879 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497879
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497879/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497879
Building REAL300025497880
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497880'
/scratch/stefan/7787277/working/building/REAL300025497880 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497880

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497880/0 /scratch/stefan/7787277/working/building/REAL300025497880 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 758)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/758
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2CC23CCOCC3)C1)

`REAL300025497880.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497880.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497880/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497880 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC23CCOCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 106, 106, 106, 106, 106, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 1, 13, 13, 106, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 48, 26, 47, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 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])
total number of confs: 200
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497880 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC23CCOCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 13, 35, 71, 101, 201, 201, 201, 201, 201, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 71, 71, 201, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48])
total number of confs: 494
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497880 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC23CCOCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 12, 5, 5, 5, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 43, 13, 1, 1, 1, 1, 1, 1, 1, 73, 106, 106, 106, 106, 106, 159, 159, 159, 201, 201, 201, 201, 201, 201, 201, 106, 43, 43, 1, 106, 106, 106, 106, 106, 159, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 106, 106] 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: 656
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497880 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497880
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497880/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497880
Building REAL300025497881
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497881'
/scratch/stefan/7787277/working/building/REAL300025497881 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497881

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497881/0 /scratch/stefan/7787277/working/building/REAL300025497881 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 759)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/759
`/scratch/stefan/7787277/working/3D/759' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCOCC1)

`REAL300025497881.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497881.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497881/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497881 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 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, 144, 144, 144, 102, 102, 102, 102, 102, 63, 30, 63, 13, 1, 1, 1, 1, 1, 1, 1, 102, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 102, 102, 102, 102, 102, 30, 30, 1, 102, 102, 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])
total number of confs: 749
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497881 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 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: [4, 1, 4, 9, 9, 9, 19, 19, 19, 19, 19, 43, 43, 80, 125, 201, 201, 201, 201, 201, 19, 1, 1, 1, 1, 1, 1, 5, 5, 5, 4, 9, 19, 19, 19, 19, 19, 80, 80, 201, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 42, 43, 44, 45, 46, 47, 48, 49, 50, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 524
number of broken/clashed sets: 49
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497881 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 6, 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: [17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 27, 102, 102, 102, 102, 102, 1, 17, 19, 19, 19, 19, 19, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 14, 14, 102, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 40, 20, 41, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 237
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497881 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497881
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497881/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497881
Building REAL300025497882
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497882'
/scratch/stefan/7787277/working/building/REAL300025497882 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497882

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497882/0 /scratch/stefan/7787277/working/building/REAL300025497882 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 760)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/760
`/scratch/stefan/7787277/working/3D/760' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CC(=O)NC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497882.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497882.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497882/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497882 none O=C(CC1CC(=O)NC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 8, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 25, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 20, 75, 75, 75, 75, 75, 1, 25, 25, 34, 34, 34, 34, 5, 1, 1, 1, 1, 1, 12, 12, 75, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 247
number of broken/clashed sets: 46
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497882 none O=C(CC1CC(=O)NC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 8, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [104, 104, 104, 191, 201, 201, 201, 201, 201, 201, 75, 75, 75, 75, 75, 48, 28, 48, 12, 1, 1, 1, 1, 1, 1, 1, 75, 191, 191, 201, 201, 201, 201, 104, 75, 75, 75, 75, 75, 28, 28, 1, 75, 75] 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, 42, 43])
total number of confs: 748
number of broken/clashed sets: 46
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497882 none O=C(CC1CC(=O)NC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 1, 11, 8, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 1, 16, 16, 34, 34, 34, 34, 34, 56, 56, 90, 130, 201, 201, 201, 201, 201, 34, 5, 5, 1, 1, 1, 1, 16, 34, 34, 34, 34, 34, 90, 90, 201, 34, 34] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 551
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497882 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497882
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497882/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497882
Building REAL300025497883
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497883'
/scratch/stefan/7787277/working/building/REAL300025497883 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497883

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497883/0 /scratch/stefan/7787277/working/building/REAL300025497883 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 761)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/761
`/scratch/stefan/7787277/working/3D/761' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC2CCC1C2)

`REAL300025497883.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497883.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497883/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497883 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC2CCC1C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 43, 126, 126, 126, 126, 126, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 21, 21, 126, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 20, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 250
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497883 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC2CCC1C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens need 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, 126, 126, 126, 126, 126, 102, 54, 102, 13, 1, 1, 1, 1, 1, 1, 1, 126, 201, 201, 201, 201, 201, 201, 201, 201, 201, 161, 126, 126, 126, 126, 126, 54, 54, 1, 126, 126, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [38, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 664
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497883 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC2CCC1C2 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 32, 32, 62, 106, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 8, 8, 8, 8, 8, 62, 62, 201, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 21, 22, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 463
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497883 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497883
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497883/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497883
Building REAL300025497884
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497884'
/scratch/stefan/7787277/working/building/REAL300025497884 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497884

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497884/0 /scratch/stefan/7787277/working/building/REAL300025497884 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 762)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/762
`/scratch/stefan/7787277/working/3D/762' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1)

`REAL300025497884.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497884.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497884/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497884 none CCC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 34, 108, 108, 108, 108, 108, 1, 5, 5, 5, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 19, 19, 108, 1, 1, 5, 5, 5] 201
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45])
total number of confs: 269
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497884 none CCC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 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, 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, 138, 138, 138, 138, 138, 138, 108, 108, 108, 108, 108, 84, 42, 84, 13, 1, 1, 1, 1, 1, 1, 1, 108, 138, 138, 138, 201, 201, 201, 201, 201, 138, 108, 108, 108, 108, 108, 42, 42, 1, 108, 108, 138, 138, 138] 201
rigid atoms, others: [40, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45])
total number of confs: 811
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497884 none CCC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 1, 1, 1, 1, 1, 2, 2, 1, 5, 5, 5, 5, 5, 16, 16, 39, 61, 138, 138, 138, 138, 138, 5, 1, 1, 1, 8, 8, 8, 8, 8, 2, 5, 5, 5, 5, 5, 39, 39, 138, 5, 5, 2, 2, 2] 201
rigid atoms, others: [1, 2, 3, 4, 5, 24, 25, 26] set([0, 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: 339
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497884 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497884
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497884/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497884
Building REAL300025497885
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497885'
/scratch/stefan/7787277/working/building/REAL300025497885 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497885

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497885/0 /scratch/stefan/7787277/working/building/REAL300025497885 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 763)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/763
`/scratch/stefan/7787277/working/3D/763' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)NCC(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497885.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497885.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497885/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497885 none CC(=O)NCC(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 6, 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, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 190, 128, 86, 128, 128, 86, 86, 50, 50, 50, 50, 50, 42, 28, 41, 13, 1, 1, 1, 1, 1, 1, 1, 50, 201, 201, 201, 201, 190, 190, 128, 128, 128, 128, 128, 128, 86, 50, 50, 50, 50, 50, 28, 28, 1, 50, 50] 201
rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49])
total number of confs: 852
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: REAL300025497885 none CC(=O)NCC(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 6, 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, 7, 7]
0  hydrogens 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, 23, 9, 5, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 15, 50, 50, 50, 50, 50, 1, 38, 38, 38, 38, 23, 23, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 9, 9, 50, 1, 1] 201
rigid atoms, others: [48, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 223
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497885 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497885
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497885/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497885
Building REAL300025497886
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497886'
/scratch/stefan/7787277/working/building/REAL300025497886 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497886

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497886/0 /scratch/stefan/7787277/working/building/REAL300025497886 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 764)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/764
`/scratch/stefan/7787277/working/3D/764' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C(C)(C)C)

`REAL300025497886.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497886.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497886/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497886 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 7, 7, 7]
0  hydrogens need 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, 86, 86, 86, 86, 86, 60, 22, 60, 13, 1, 1, 1, 1, 1, 1, 1, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 86, 86, 86, 86, 86, 22, 22, 1, 86, 86, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [39, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 644
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: REAL300025497886 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C(C)(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
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, 7, 7, 7]
0  hydrogens 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, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 36, 86, 86, 86, 86, 86, 1, 8, 8, 8, 9, 9, 9, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 19, 19, 86, 1, 1, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 40, 20, 41, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 201
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497886 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497886
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497886/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497886
Building REAL300025497887
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497887'
/scratch/stefan/7787277/working/building/REAL300025497887 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497887

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497887/0 /scratch/stefan/7787277/working/building/REAL300025497887 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 765)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/765
`/scratch/stefan/7787277/working/3D/765' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC1=CC=CO1)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497887.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497887.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497887/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497887 none CC(CC1=CC=CO1)C(=O)NC1C=CCN(C(=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', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 16, 26, 39, 39, 39, 39, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 11, 46, 46, 46, 46, 46, 1, 16, 16, 16, 16, 26, 26, 39, 39, 39, 5, 1, 1, 1, 1, 1, 6, 6, 46, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 195
number of broken/clashed sets: 41
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497887 none CC(CC1=CC=CO1)C(=O)NC1C=CCN(C(=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', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [169, 77, 169, 192, 201, 201, 201, 201, 77, 77, 46, 46, 46, 46, 46, 43, 27, 43, 12, 1, 1, 1, 1, 1, 1, 1, 46, 169, 169, 169, 169, 192, 192, 201, 201, 201, 77, 46, 46, 46, 46, 46, 27, 27, 1, 46, 46] 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])
total number of confs: 833
number of broken/clashed sets: 41
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497887 none CC(CC1=CC=CO1)C(=O)NC1C=CCN(C(=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', 'C.2', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 12, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 26, 26, 26, 39, 39, 39, 39, 39, 46, 46, 84, 123, 201, 201, 201, 201, 201, 39, 10, 10, 10, 10, 3, 3, 1, 1, 1, 26, 39, 39, 39, 39, 39, 84, 84, 201, 39, 39] 201
rigid atoms, others: [33, 2, 3, 4, 5, 6, 7, 34, 35] 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, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 553
number of broken/clashed sets: 41
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497887 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497887
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497887/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497887
Building REAL300025497888
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497888'
/scratch/stefan/7787277/working/building/REAL300025497888 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497888

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497888/0 /scratch/stefan/7787277/working/building/REAL300025497888 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 766)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/766
`/scratch/stefan/7787277/working/3D/766' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCC(=O)N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497888.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497888.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497888/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497888 none O=C(CC1CCC(=O)N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 22, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 25, 84, 84, 84, 84, 84, 1, 22, 22, 36, 36, 36, 36, 36, 36, 5, 1, 1, 1, 1, 1, 13, 13, 84, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 263
number of broken/clashed sets: 64
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497888 none O=C(CC1CCC(=O)N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [118, 118, 118, 193, 201, 201, 201, 201, 201, 84, 84, 84, 84, 84, 54, 29, 54, 13, 1, 1, 1, 1, 1, 1, 1, 84, 193, 193, 201, 201, 201, 201, 201, 201, 118, 84, 84, 84, 84, 84, 29, 29, 1, 84, 84] 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])
total number of confs: 746
number of broken/clashed sets: 64
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497888 none O=C(CC1CCC(=O)N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 5, 1, 1, 1, 1, 1, 1, 1, 22, 22, 36, 36, 36, 36, 36, 48, 48, 84, 126, 201, 201, 201, 201, 201, 36, 5, 5, 1, 1, 1, 1, 1, 1, 22, 36, 36, 36, 36, 36, 84, 84, 201, 36, 36] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 546
number of broken/clashed sets: 64
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497888 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497888
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497888/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497888
Building REAL300025497889
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497889'
/scratch/stefan/7787277/working/building/REAL300025497889 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497889

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497889/0 /scratch/stefan/7787277/working/building/REAL300025497889 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 767)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/767
`/scratch/stefan/7787277/working/3D/767' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN3C=CN=C23)C1)

`REAL300025497889.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497889.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497889/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497889 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN3C=CN=C23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 6, 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, 21, 47, 141, 141, 141, 141, 141, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 1, 21, 21, 141, 1, 1, 1, 1, 1, 5, 9, 9, 9, 9, 9, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 260
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497889 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN3C=CN=C23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 6, 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: [30, 9, 30, 63, 111, 201, 201, 201, 201, 201, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 63, 63, 201, 9, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 9, 9] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 453
number of broken/clashed sets: 33
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497889 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN3C=CN=C23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 6, 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: [103, 43, 13, 1, 1, 1, 1, 1, 1, 1, 103, 141, 141, 141, 141, 141, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 141, 43, 43, 1, 141, 141, 141, 141, 141, 200, 201, 201, 201, 201, 201, 141, 141] 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: 612
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497889 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497889
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497889/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497889
Building REAL300025497890
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497890'
/scratch/stefan/7787277/working/building/REAL300025497890 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497890

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497890/0 /scratch/stefan/7787277/working/building/REAL300025497890 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 768)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/768
`/scratch/stefan/7787277/working/3D/768' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)C1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1)

`REAL300025497890.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497890.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497890/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497890 none CNC(=O)C1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 17, 22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 30, 67, 67, 67, 67, 67, 1, 17, 17, 22, 22, 22, 22, 5, 1, 1, 1, 1, 1, 20, 20, 67, 1, 1, 17, 17, 17, 17] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 40, 23, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44])
total number of confs: 205
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497890 none CNC(=O)C1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 99, 99, 99, 67, 67, 67, 67, 67, 52, 32, 52, 13, 1, 1, 1, 1, 1, 1, 1, 67, 201, 201, 201, 201, 201, 201, 99, 67, 67, 67, 67, 67, 32, 32, 1, 67, 67, 201, 201, 201, 201] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44])
total number of confs: 628
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497890 none CNC(=O)C1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 17, 17, 17, 17, 17, 46, 46, 92, 132, 201, 201, 201, 201, 201, 17, 1, 1, 5, 5, 5, 5, 5, 17, 17, 17, 17, 17, 92, 92, 201, 17, 17, 1, 1, 1, 1] 201
rigid atoms, others: [2, 4, 5, 41, 42, 43, 44, 24, 25] set([0, 1, 3, 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])
total number of confs: 539
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497890 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497890
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497890/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497890
Building REAL300025497891
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497891'
/scratch/stefan/7787277/working/building/REAL300025497891 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497891

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497891/0 /scratch/stefan/7787277/working/building/REAL300025497891 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 769)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/769
`/scratch/stefan/7787277/working/3D/769' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1F)

`REAL300025497891.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497891.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497891/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497891 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 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: [15, 15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 25, 67, 67, 67, 67, 67, 1, 15, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 15, 15, 67, 1, 1, 15] 201
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 157
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497891 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 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, 80, 80, 80, 67, 67, 67, 67, 67, 53, 38, 53, 11, 1, 1, 1, 1, 1, 1, 1, 67, 201, 201, 201, 201, 201, 201, 201, 201, 80, 67, 67, 67, 67, 67, 38, 38, 1, 67, 67, 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])
total number of confs: 439
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497891 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1F NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 15, 7, 7, 7, 7, 7, 6, 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, 5, 5, 5, 15, 15, 15, 15, 15, 34, 34, 70, 105, 201, 201, 201, 201, 201, 15, 1, 1, 1, 2, 2, 2, 1, 1, 5, 15, 15, 15, 15, 15, 70, 70, 201, 15, 15, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 506
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497891 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497891
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497891/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497891
Building REAL300025497892
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497892'
/scratch/stefan/7787277/working/building/REAL300025497892 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497892

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497892/0 /scratch/stefan/7787277/working/building/REAL300025497892 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 770)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/770
`/scratch/stefan/7787277/working/3D/770' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1)

`REAL300025497892.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497892.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497892/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497892 none CC1=C(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 27, 60, 60, 60, 60, 60, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 16, 16, 60, 1, 1, 21, 21, 21] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46])
total number of confs: 156
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497892 none CC1=C(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 73, 73, 73, 60, 60, 60, 60, 60, 52, 34, 52, 13, 1, 1, 1, 1, 1, 1, 1, 60, 201, 201, 201, 201, 201, 201, 201, 201, 201, 73, 60, 60, 60, 60, 60, 34, 34, 1, 60, 60, 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])
total number of confs: 431
number of broken/clashed sets: 29
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497892 none CC1=C(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 21, 21, 21, 21, 21, 53, 53, 92, 138, 201, 201, 201, 201, 201, 21, 1, 1, 1, 2, 2, 2, 2, 2, 2, 9, 21, 21, 21, 21, 21, 92, 92, 201, 21, 21, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 26] set([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: 549
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497892 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497892
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497892/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497892
Building REAL300025497893
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497893'
/scratch/stefan/7787277/working/building/REAL300025497893 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497893

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497893/0 /scratch/stefan/7787277/working/building/REAL300025497893 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 771)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/771
`/scratch/stefan/7787277/working/3D/771' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1)

`REAL300025497893.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497893.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497893/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497893 none COC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 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, 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, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 34, 141, 141, 141, 141, 141, 1, 12, 12, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 15, 15, 141, 1, 1, 12] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 241
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497893 none COC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 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, 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, 170, 170, 170, 141, 141, 141, 141, 141, 104, 55, 104, 13, 1, 1, 1, 1, 1, 1, 1, 141, 201, 201, 201, 201, 201, 201, 201, 170, 141, 141, 141, 141, 141, 55, 55, 1, 141, 141, 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])
total number of confs: 571
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497893 none COC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 36, 36, 68, 112, 201, 201, 201, 201, 201, 12, 1, 1, 2, 2, 2, 1, 1, 5, 12, 12, 12, 12, 12, 68, 68, 201, 12, 12, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 43, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 492
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497893 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497893
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497893/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497893
Building REAL300025497894
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497894'
/scratch/stefan/7787277/working/building/REAL300025497894 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497894

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497894/0 /scratch/stefan/7787277/working/building/REAL300025497894 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 772)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/772
`/scratch/stefan/7787277/working/3D/772' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C)=NN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497894.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497894.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497894/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497894 none CC1=CC(C)=NN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens 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, 19, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 26, 98, 98, 98, 98, 98, 1, 19, 19, 19, 19, 19, 19, 19, 16, 16, 5, 1, 1, 1, 1, 1, 15, 15, 98, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 220
number of broken/clashed sets: 38
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497894 none CC1=CC(C)=NN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 199, 118, 118, 118, 98, 98, 98, 98, 98, 56, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 98, 201, 201, 201, 201, 201, 201, 201, 199, 199, 118, 98, 98, 98, 98, 98, 29, 29, 1, 98, 98] 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])
total number of confs: 744
number of broken/clashed sets: 38
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497894 none CC1=CC(C)=NN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 5, 8, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total 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, 11, 11, 11, 19, 19, 19, 19, 19, 41, 41, 74, 116, 201, 201, 201, 201, 201, 19, 2, 2, 2, 1, 2, 2, 2, 4, 4, 11, 19, 19, 19, 19, 19, 74, 74, 201, 19, 19] 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: 527
number of broken/clashed sets: 38
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497894 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497894
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497894/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497894
Building REAL300025497895
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497895'
/scratch/stefan/7787277/working/building/REAL300025497895 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497895

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497895/0 /scratch/stefan/7787277/working/building/REAL300025497895 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 773)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/773
`/scratch/stefan/7787277/working/3D/773' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1)

`REAL300025497895.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497895.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497895/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497895 none COCC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [29, 19, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 24, 79, 79, 79, 79, 79, 1, 5, 29, 29, 29, 19, 19, 5, 5, 5, 1, 1, 1, 1, 1, 13, 13, 79, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 227
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497895 none COCC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 91, 91, 91, 91, 91, 91, 91, 79, 79, 79, 79, 79, 67, 39, 67, 13, 1, 1, 1, 1, 1, 1, 1, 79, 91, 201, 201, 201, 201, 201, 91, 91, 91, 79, 79, 79, 79, 79, 39, 39, 1, 79, 79] 201
rigid atoms, others: [42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44])
total number of confs: 823
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497895 none COCC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 9, 9, 17, 30, 91, 91, 91, 91, 91, 5, 1, 14, 14, 14, 7, 7, 1, 1, 1, 5, 5, 5, 5, 5, 17, 17, 91, 5, 5] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 26] set([0, 1, 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])
total number of confs: 202
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497895 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497895
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497895/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497895
Building REAL300025497896
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497896'
/scratch/stefan/7787277/working/building/REAL300025497896 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497896

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497896/0 /scratch/stefan/7787277/working/building/REAL300025497896 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 774)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/774
`/scratch/stefan/7787277/working/3D/774' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(Cl)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497896.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497896.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497896/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497896 none CN1C=C(Cl)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 4, 4, 17, 47, 149, 149, 149, 149, 149, 1, 12, 12, 12, 12, 12, 6, 1, 1, 1, 1, 1, 17, 17, 149, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 264
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497896 none CN1C=C(Cl)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 199, 199, 199, 149, 149, 149, 149, 149, 125, 51, 125, 13, 1, 1, 1, 1, 1, 1, 1, 149, 201, 201, 201, 201, 201, 199, 149, 149, 149, 149, 149, 51, 51, 1, 149, 149] 201
rigid atoms, others: [39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41])
total number of confs: 603
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497896 none CN1C=C(Cl)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 1, 16, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 12, 12, 12, 12, 12, 26, 26, 63, 115, 201, 201, 201, 201, 201, 12, 2, 2, 2, 1, 1, 4, 12, 12, 12, 12, 12, 63, 63, 201, 12, 12] 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])
total number of confs: 473
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497896 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497896
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497896/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497896
Building REAL300025497897
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497897'
/scratch/stefan/7787277/working/building/REAL300025497897 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497897

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497897/0 /scratch/stefan/7787277/working/building/REAL300025497897 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 775)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/775
`/scratch/stefan/7787277/working/3D/775' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=NC=CN3C=C2)C1)

`REAL300025497897.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497897.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497897/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497897 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=NC=CN3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 1, 5, 7, 7, 6, 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: [5, 1, 5, 15, 30, 90, 90, 90, 90, 90, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 1, 15, 15, 90, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 188
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497897 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=NC=CN3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 1, 5, 7, 7, 6, 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: [33, 15, 33, 71, 112, 201, 201, 201, 201, 201, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 71, 71, 201, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 15, 15] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 500
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497897 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=NC=CN3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 1, 1, 5, 7, 7, 6, 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: [69, 48, 13, 1, 1, 1, 1, 1, 1, 1, 69, 90, 90, 90, 90, 90, 108, 108, 108, 201, 201, 201, 201, 201, 201, 201, 201, 90, 48, 48, 1, 90, 90, 90, 90, 90, 108, 201, 201, 201, 201, 201, 90, 90] 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: 494
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497897 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497897
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497897/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497897
Building REAL300025497898
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497898'
/scratch/stefan/7787277/working/building/REAL300025497898 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497898

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497898/0 /scratch/stefan/7787277/working/building/REAL300025497898 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 776)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/776
`/scratch/stefan/7787277/working/3D/776' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC3=NC=CN32)C1)

`REAL300025497898.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497898.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497898/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497898 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC3=NC=CN32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 7, 7, 6, 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: [5, 1, 5, 12, 21, 71, 71, 71, 71, 71, 1, 1, 1, 1, 1, 1, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 1, 12, 12, 71, 1, 1, 1, 1, 1, 5, 21, 21, 21, 21, 21, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 154
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497898 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC3=NC=CN32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 7, 7, 6, 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: [48, 21, 48, 87, 116, 201, 201, 201, 201, 201, 21, 21, 21, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 87, 87, 201, 21, 21, 21, 21, 21, 9, 1, 1, 1, 1, 1, 21, 21] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 532
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497898 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC3=NC=CN32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 1, 8, 5, 7, 7, 6, 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: [51, 35, 13, 1, 1, 1, 1, 1, 1, 1, 51, 71, 71, 71, 71, 71, 100, 100, 100, 201, 201, 201, 201, 201, 201, 201, 201, 71, 35, 35, 1, 71, 71, 71, 71, 71, 100, 201, 201, 201, 201, 201, 71, 71] 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: 480
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497898 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497898
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497898/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497898
Building REAL300025497899
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497899'
/scratch/stefan/7787277/working/building/REAL300025497899 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497899

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497899/0 /scratch/stefan/7787277/working/building/REAL300025497899 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 777)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/777
`/scratch/stefan/7787277/working/3D/777' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3NC=CC3=N2)C1)

`REAL300025497899.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497899.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497899/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497899 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3NC=CC3=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 55, 143, 143, 143, 143, 143, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 1, 32, 32, 143, 1, 1, 1, 1, 1, 5, 10, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 299
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497899 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3NC=CC3=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 10, 32, 82, 120, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 82, 82, 201, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 510
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497899 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3NC=CC3=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'C.2', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 42, 13, 1, 1, 1, 1, 1, 1, 1, 104, 143, 143, 143, 143, 143, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 201, 143, 42, 42, 1, 143, 143, 143, 143, 143, 200, 201, 201, 201, 201, 201, 143, 143] 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: 602
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497899 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497899/1 /scratch/stefan/7787277/working/building/REAL300025497899 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 778)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/778
`/scratch/stefan/7787277/working/3D/778' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3N=CC=C3N2)C1)

`REAL300025497899.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497899.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497899/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497899 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3N=CC=C3N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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: [5, 1, 5, 18, 32, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 1, 18, 18, 72, 1, 1, 1, 1, 1, 5, 22, 22, 22, 22, 22, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 184
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497899 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3N=CC=C3N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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: [52, 22, 52, 95, 140, 201, 201, 201, 201, 201, 22, 22, 22, 22, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 95, 95, 201, 22, 22, 22, 22, 22, 8, 1, 1, 1, 1, 1, 22, 22] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 559
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497899 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C3N=CC=C3N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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: [61, 36, 13, 1, 1, 1, 1, 1, 1, 1, 61, 72, 72, 72, 72, 72, 92, 92, 92, 201, 201, 201, 201, 201, 201, 201, 201, 72, 36, 36, 1, 72, 72, 72, 72, 72, 92, 201, 201, 201, 201, 201, 72, 72] 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: 470
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497899 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497899
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497899/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497899/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497899
Building REAL300025497900
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497900'
/scratch/stefan/7787277/working/building/REAL300025497900 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497900

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497900/0 /scratch/stefan/7787277/working/building/REAL300025497900 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 779)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/779
`/scratch/stefan/7787277/working/3D/779' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497900.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497900.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497900/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497900 none CC1=NN(C)C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [24, 24, 24, 24, 24, 20, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 19, 83, 83, 83, 83, 83, 1, 24, 24, 24, 24, 24, 24, 24, 20, 20, 4, 1, 1, 1, 1, 1, 11, 11, 83, 1, 1, 24] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46])
total number of confs: 207
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497900 none CC1=NN(C)C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 196, 101, 101, 101, 83, 83, 83, 83, 83, 49, 29, 49, 13, 1, 1, 1, 1, 1, 1, 1, 83, 201, 201, 201, 201, 201, 201, 201, 196, 196, 101, 83, 83, 83, 83, 83, 29, 29, 1, 83, 83, 201] 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: 742
number of broken/clashed sets: 39
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497900 none CC1=NN(C)C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 13, 13, 13, 24, 24, 24, 24, 24, 50, 50, 80, 115, 201, 201, 201, 201, 201, 24, 1, 2, 2, 2, 2, 2, 2, 4, 4, 13, 24, 24, 24, 24, 24, 80, 80, 201, 24, 24, 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: 539
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497900 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497900
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497900/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497900
Building REAL300025497901
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497901'
/scratch/stefan/7787277/working/building/REAL300025497901 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497901

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497901/0 /scratch/stefan/7787277/working/building/REAL300025497901 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 780)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/780
`/scratch/stefan/7787277/working/3D/780' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=C3C=CC=CN32)C1)

`REAL300025497901.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497901.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497901/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497901 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=C3C=CC=CN32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 6, 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, 30, 54, 149, 149, 149, 149, 149, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 12, 12, 12, 12, 12, 12, 1, 30, 30, 149, 1, 1, 1, 1, 1, 6, 12, 12, 12, 12, 12, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 302
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497901 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=C3C=CC=CN32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 6, 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, 12, 35, 88, 123, 201, 201, 201, 201, 201, 12, 12, 12, 12, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 88, 88, 201, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 12, 12] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 528
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497901 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=C3C=CC=CN32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 1, 1, 8, 5, 7, 7, 6, 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: [106, 44, 13, 1, 1, 1, 1, 1, 1, 1, 106, 149, 149, 149, 149, 149, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 44, 44, 1, 149, 149, 149, 149, 149, 201, 201, 201, 201, 201, 201, 149, 149] 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: 612
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497901 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497901
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497901/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497901
Building REAL300025497902
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497902'
/scratch/stefan/7787277/working/building/REAL300025497902 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497902

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497902/0 /scratch/stefan/7787277/working/building/REAL300025497902 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 781)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/781
`/scratch/stefan/7787277/working/3D/781' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1)

`REAL300025497902.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497902.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497902/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497902 none COCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [37, 22, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 23, 81, 81, 81, 81, 81, 1, 11, 11, 37, 37, 37, 22, 22, 4, 1, 1, 1, 1, 1, 12, 12, 81, 1, 1, 11, 11, 11, 11] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44])
total number of confs: 237
number of broken/clashed sets: 64
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497902 none COCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
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, 127, 127, 127, 81, 81, 81, 81, 81, 66, 31, 66, 13, 1, 1, 1, 1, 1, 1, 1, 81, 193, 193, 201, 201, 201, 201, 201, 127, 81, 81, 81, 81, 81, 31, 31, 1, 81, 81, 193, 193, 193, 193] 201
rigid atoms, others: [38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44])
total number of confs: 652
number of broken/clashed sets: 64
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497902 none COCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 11, 18, 18, 51, 92, 193, 193, 193, 193, 193, 11, 1, 1, 17, 17, 17, 7, 7, 6, 11, 11, 11, 11, 11, 51, 51, 193, 11, 11, 1, 1, 1, 1] 201
rigid atoms, others: [2, 3, 4, 41, 42, 43, 44, 23, 24] set([0, 1, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 456
number of broken/clashed sets: 64
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497902 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497902
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497902/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497902
Building REAL300025497903
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497903'
/scratch/stefan/7787277/working/building/REAL300025497903 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497903

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497903/0 /scratch/stefan/7787277/working/building/REAL300025497903 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 782)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/782
`/scratch/stefan/7787277/working/3D/782' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497903.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497903.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497903/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497903 none COCC(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
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, 125, 176, 176, 125, 125, 91, 91, 91, 91, 91, 64, 28, 63, 13, 1, 1, 1, 1, 1, 1, 1, 91, 201, 201, 201, 201, 201, 176, 176, 176, 176, 176, 176, 125, 91, 91, 91, 91, 91, 28, 28, 1, 91, 91] 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])
total number of confs: 793
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497903 none COCC(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 16, 10, 4, 10, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 30, 91, 91, 91, 91, 91, 1, 26, 26, 26, 16, 16, 10, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 17, 17, 91, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 251
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497903 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497903
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497903/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497903
Building REAL300025497904
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497904'
/scratch/stefan/7787277/working/building/REAL300025497904 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497904

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497904/0 /scratch/stefan/7787277/working/building/REAL300025497904 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 783)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/783
`/scratch/stefan/7787277/working/3D/783' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=NOC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497904.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497904.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497904/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497904 none O=C(CCC1=NOC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 12, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 19, 26, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 26, 84, 84, 84, 84, 84, 1, 19, 19, 26, 26, 33, 33, 5, 1, 1, 1, 1, 1, 13, 13, 84, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 267
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497904 none O=C(CCC1=NOC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 12, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 193, 197, 201, 201, 201, 201, 84, 84, 84, 84, 84, 52, 29, 52, 12, 1, 1, 1, 1, 1, 1, 1, 84, 193, 193, 197, 197, 201, 201, 132, 84, 84, 84, 84, 84, 29, 29, 1, 84, 84] 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])
total number of confs: 714
number of broken/clashed sets: 63
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497904 none O=C(CCC1=NOC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 12, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 4, 1, 1, 1, 1, 1, 1, 19, 19, 33, 33, 33, 33, 33, 46, 46, 86, 125, 201, 201, 201, 201, 201, 33, 6, 6, 4, 4, 1, 1, 19, 33, 33, 33, 33, 33, 86, 86, 201, 33, 33] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 537
number of broken/clashed sets: 63
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497904 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497904
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497904/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497904
Building REAL300025497905
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497905'
/scratch/stefan/7787277/working/building/REAL300025497905 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497905

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497905/0 /scratch/stefan/7787277/working/building/REAL300025497905 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 784)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/784
`/scratch/stefan/7787277/working/3D/784' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CN=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497905.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497905.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497905/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497905 none O=C(CCC1=CN=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 1, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 23, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 26, 78, 78, 78, 78, 78, 1, 23, 23, 26, 26, 26, 26, 26, 5, 1, 1, 1, 1, 1, 14, 14, 78, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 44, 10, 11, 12, 13, 14, 15, 16, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 233
number of broken/clashed sets: 51
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497905 none O=C(CCC1=CN=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 1, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 183, 201, 201, 201, 201, 201, 201, 78, 78, 78, 78, 78, 49, 28, 49, 13, 1, 1, 1, 1, 1, 1, 1, 78, 183, 183, 201, 201, 201, 201, 201, 94, 78, 78, 78, 78, 78, 28, 28, 1, 78, 78] 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, 43, 44])
total number of confs: 783
number of broken/clashed sets: 51
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497905 none O=C(CCC1=CN=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 8, 1, 8, 1, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 3, 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]
0  hydrogens 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, 2, 1, 1, 1, 1, 1, 1, 1, 19, 19, 40, 40, 40, 40, 40, 50, 50, 93, 131, 201, 201, 201, 201, 201, 40, 6, 6, 2, 2, 1, 1, 1, 19, 40, 40, 40, 40, 40, 93, 93, 201, 40, 40] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 556
number of broken/clashed sets: 72
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497905 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497905
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497905/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497905
Building REAL300025497906
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497906'
/scratch/stefan/7787277/working/building/REAL300025497906 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497906

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497906/0 /scratch/stefan/7787277/working/building/REAL300025497906 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 785)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/785
`/scratch/stefan/7787277/working/3D/785' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN3C=[NH+]C=C3C=C2)C1)

`REAL300025497906.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497906.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497906/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497906 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN3C=[NH+]C=C3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 1, 1, 1, 5, 7, 7, 6, 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]
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: [5, 1, 5, 11, 19, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 11, 11, 40, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 8, 1, 1] 60
rigid atoms, others: [32, 1, 34, 35, 36, 33, 44, 10, 11, 12, 13, 14, 15, 43, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 37, 38, 39, 40, 41, 42])
total number of confs: 102
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497906 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN3C=[NH+]C=C3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 1, 1, 1, 5, 7, 7, 6, 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]
0  hydrogens need rotated
60  conformations in input
total number of sets (complete confs): 60
using faster count positions algorithm for large data
unique positions, atoms: [15, 8, 15, 26, 39, 60, 60, 60, 60, 60, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 26, 26, 60, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 8, 8] 60
rigid atoms, others: [38, 39, 40, 41, 42, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44])
total number of confs: 162
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497906 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN3C=[NH+]C=C3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.cat', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 1, 1, 1, 5, 7, 7, 6, 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]
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: [34, 32, 12, 1, 1, 1, 1, 1, 1, 1, 34, 40, 40, 40, 40, 40, 45, 45, 45, 60, 60, 60, 60, 60, 60, 60, 60, 60, 40, 32, 32, 1, 40, 40, 40, 40, 40, 45, 60, 60, 60, 60, 60, 40, 40] 60
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])
total number of confs: 170
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497906 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497906/1 /scratch/stefan/7787277/working/building/REAL300025497906 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 786)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/786
`/scratch/stefan/7787277/working/3D/786' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN3C=NC=C3C=C2)C1)

`REAL300025497906.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497906.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497906/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497906 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN3C=NC=C3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 7, 7, 6, 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: [5, 1, 5, 15, 29, 91, 91, 91, 91, 91, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 1, 15, 15, 91, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 186
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497906 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN3C=NC=C3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 7, 7, 6, 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: [37, 13, 37, 70, 107, 201, 201, 201, 201, 201, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 70, 70, 201, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 13, 13] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 490
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497906 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN3C=NC=C3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 7, 7, 6, 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: [73, 50, 13, 1, 1, 1, 1, 1, 1, 1, 73, 91, 91, 91, 91, 91, 107, 107, 107, 201, 201, 201, 201, 201, 201, 201, 201, 91, 50, 50, 1, 91, 91, 91, 91, 91, 107, 201, 201, 201, 201, 201, 91, 91] 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: 495
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497906 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497906
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497906/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497906/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497906
Building REAL300025497907
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497907'
/scratch/stefan/7787277/working/building/REAL300025497907 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497907

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497907/0 /scratch/stefan/7787277/working/building/REAL300025497907 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 787)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/787
`/scratch/stefan/7787277/working/3D/787' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CN=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497907.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497907.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497907/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497907 none CCC1=CN=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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: [21, 11, 11, 11, 11, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 32, 84, 84, 84, 84, 84, 1, 11, 21, 21, 21, 21, 21, 11, 11, 4, 1, 1, 1, 1, 1, 21, 21, 84, 1, 1, 11] 201
rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45])
total number of confs: 246
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497907 none CCC1=CN=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 131, 131, 131, 131, 131, 94, 94, 94, 84, 84, 84, 84, 84, 74, 42, 74, 13, 1, 1, 1, 1, 1, 1, 1, 84, 131, 201, 201, 201, 201, 201, 131, 131, 94, 84, 84, 84, 84, 84, 42, 42, 1, 84, 84, 131] 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: 783
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497907 none CCC1=CN=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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: [2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 11, 11, 11, 11, 24, 24, 53, 73, 131, 131, 131, 131, 131, 11, 1, 2, 2, 2, 2, 2, 1, 1, 5, 11, 11, 11, 11, 11, 53, 53, 131, 11, 11, 1] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 33, 7, 45, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 340
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497907 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497907
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497907/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497907
Building REAL300025497908
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497908'
/scratch/stefan/7787277/working/building/REAL300025497908 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497908

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497908/0 /scratch/stefan/7787277/working/building/REAL300025497908 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 788)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/788
`/scratch/stefan/7787277/working/3D/788' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC(=O)NC(=O)C2)C1)

`REAL300025497908.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497908.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497908/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497908 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC(=O)NC(=O)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 13, 22, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 5, 5, 5, 20, 20, 20, 20, 20, 20, 20, 1, 13, 13, 76, 1, 1, 1, 1, 1, 5, 20, 20, 20, 20, 20, 20, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 10, 11, 12, 13, 14, 15, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 179
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497908 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC(=O)NC(=O)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 20, 45, 88, 120, 201, 201, 201, 201, 201, 20, 20, 20, 20, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 20, 88, 88, 201, 20, 20, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 20, 20] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 16, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42, 43])
total number of confs: 548
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497908 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC(=O)NC(=O)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 1, 11, 8, 1, 11, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [53, 36, 13, 1, 1, 1, 1, 1, 1, 1, 53, 76, 76, 76, 76, 76, 117, 117, 117, 201, 201, 201, 201, 201, 201, 201, 76, 36, 36, 1, 76, 76, 76, 76, 76, 117, 201, 201, 201, 201, 201, 201, 76, 76] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 654
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497908 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497908
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497908/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497908
Building REAL300025497909
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497909'
/scratch/stefan/7787277/working/building/REAL300025497909 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497909

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497909/0 /scratch/stefan/7787277/working/building/REAL300025497909 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 789)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/789
`/scratch/stefan/7787277/working/3D/789' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025497909.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497909.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497909/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497909 none CN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 6, 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, 6, 7, 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: [9, 9, 9, 9, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 36, 62, 157, 157, 157, 157, 157, 1, 9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 36, 36, 157, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 7, 8, 9, 10, 11, 12, 13, 23, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 327
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497909 none CN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 157, 157, 157, 157, 157, 111, 44, 111, 13, 1, 1, 1, 1, 1, 1, 1, 157, 201, 201, 201, 201, 201, 201, 157, 157, 157, 157, 157, 44, 44, 1, 157, 157] 201
rigid atoms, others: [37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 597
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497909 none CN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 9, 9, 9, 9, 9, 30, 30, 86, 119, 201, 201, 201, 201, 201, 9, 1, 2, 2, 2, 1, 4, 9, 9, 9, 9, 9, 86, 86, 201, 9, 9] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 528
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497909 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497909
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497909/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497909
Building REAL300025497910
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497910'
/scratch/stefan/7787277/working/building/REAL300025497910 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497910

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497910/0 /scratch/stefan/7787277/working/building/REAL300025497910 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 790)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/790
`/scratch/stefan/7787277/working/3D/790' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CC(Cl)=C2)C1)

`REAL300025497910.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497910.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497910/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497910 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CC(Cl)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 16, 1, 5, 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, 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, 12, 28, 88, 88, 88, 88, 88, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 1, 12, 12, 88, 1, 1, 1, 1, 1, 4, 13, 13, 13, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497910 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CC(Cl)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 16, 1, 5, 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, 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, 13, 30, 67, 108, 201, 201, 201, 201, 201, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 13, 67, 67, 201, 13, 13, 13, 13, 13, 5, 1, 1, 1, 13, 13] 201
rigid atoms, others: [35, 36, 37, 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, 38, 39])
total number of confs: 487
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497910 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CC(Cl)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 16, 1, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [73, 42, 13, 1, 1, 1, 1, 1, 1, 1, 73, 88, 88, 88, 88, 88, 108, 108, 108, 201, 201, 201, 201, 201, 201, 88, 42, 42, 1, 88, 88, 88, 88, 88, 108, 201, 201, 201, 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])
total number of confs: 498
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497910 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497910
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497910/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497910
Building REAL300025497911
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497911'
/scratch/stefan/7787277/working/building/REAL300025497911 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497911

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497911/0 /scratch/stefan/7787277/working/building/REAL300025497911 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 791)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/791
`/scratch/stefan/7787277/working/3D/791' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CS1)

`REAL300025497911.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497911.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497911/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497911 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 14, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 25, 102, 102, 102, 102, 102, 1, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 15, 15, 102, 1, 1, 15] 201
rigid atoms, others: [32, 33, 34, 38, 6, 7, 8, 9, 10, 11, 12, 22, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40])
total number of confs: 195
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497911 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 14, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 127, 127, 127, 102, 102, 102, 102, 102, 80, 52, 80, 13, 1, 1, 1, 1, 1, 1, 1, 102, 201, 201, 201, 201, 201, 201, 127, 102, 102, 102, 102, 102, 52, 52, 1, 102, 102, 201] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 550
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497911 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CS1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 14, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 15, 15, 15, 15, 15, 35, 35, 72, 106, 201, 201, 201, 201, 201, 15, 1, 1, 2, 2, 2, 1, 5, 15, 15, 15, 15, 15, 72, 72, 201, 15, 15, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 40, 23, 24, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 506
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497911 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497911
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497911/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497911
Building REAL300025497912
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497912'
/scratch/stefan/7787277/working/building/REAL300025497912 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497912

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497912/0 /scratch/stefan/7787277/working/building/REAL300025497912 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 792)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/792
`/scratch/stefan/7787277/working/3D/792' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCN1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497912.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497912.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497912/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497912 none O=C(CCN1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens 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, 21, 21, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 13, 48, 48, 48, 48, 48, 1, 21, 21, 21, 21, 35, 35, 35, 35, 35, 35, 35, 35, 5, 1, 1, 1, 1, 1, 6, 6, 48, 1, 1] 201
rigid atoms, others: [48, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 170
number of broken/clashed sets: 62
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497912 none O=C(CCN1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens 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, 135, 135, 201, 201, 201, 201, 201, 48, 48, 48, 48, 48, 40, 24, 40, 13, 1, 1, 1, 1, 1, 1, 1, 48, 135, 135, 135, 135, 201, 201, 201, 201, 201, 201, 201, 201, 72, 48, 48, 48, 48, 48, 24, 24, 1, 48, 48] 201
rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49])
total number of confs: 683
number of broken/clashed sets: 62
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497912 none O=C(CCN1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 10, 5, 5, 12, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 3, 3, 1, 1, 1, 1, 1, 1, 1, 19, 19, 35, 35, 35, 35, 35, 53, 53, 98, 145, 201, 201, 201, 201, 201, 35, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 19, 35, 35, 35, 35, 35, 98, 98, 201, 35, 35] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 38, 37, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 580
number of broken/clashed sets: 62
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497912 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497912/1 /scratch/stefan/7787277/working/building/REAL300025497912 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 793)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/793
`/scratch/stefan/7787277/working/3D/793' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC[NH+]1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497912.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497912.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497912/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497912 none O=C(CC[NH+]1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 9, 6, 5, 5, 12, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 1, 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]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 12, 23, 23, 23, 23, 23, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 8, 8, 23, 1, 1] 36
rigid atoms, others: [45, 43, 49, 41, 42, 11, 12, 13, 14, 15, 16, 17, 50, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48])
total number of confs: 88
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497912 none O=C(CC[NH+]1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 9, 6, 5, 5, 12, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 1, 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]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [28, 28, 28, 36, 36, 36, 36, 36, 36, 36, 36, 23, 23, 23, 23, 23, 23, 20, 23, 13, 1, 1, 1, 1, 1, 1, 1, 23, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 28, 23, 23, 23, 23, 23, 20, 20, 1, 23, 23] 36
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, 49, 50])
total number of confs: 127
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497912 none O=C(CC[NH+]1CCOCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [11, 1, 5, 5, 9, 6, 5, 5, 12, 5, 5, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 1, 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]
0  hydrogens need rotated
36  conformations in input
total number of sets (complete confs): 36
using default count positions algorithm for smaller data
unique positions, atoms: [6, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 11, 14, 14, 24, 29, 36, 36, 36, 36, 36, 11, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 11, 11, 24, 24, 36, 11, 11] 36
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 10, 39, 35, 36, 38, 37] set([0, 1, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 115
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497912 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497912
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497912/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497912/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497912
Building REAL300025497913
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497913'
/scratch/stefan/7787277/working/building/REAL300025497913 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497913

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497913/0 /scratch/stefan/7787277/working/building/REAL300025497913 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 794)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/794
`/scratch/stefan/7787277/working/3D/794' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COC1=CC=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497913.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497913.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497913/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497913 none O=C(COC1=CC=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 3, 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]
0  hydrogens 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, 25, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 11, 52, 52, 52, 52, 52, 1, 10, 10, 41, 41, 41, 41, 4, 1, 1, 1, 1, 1, 5, 5, 52, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 158
number of broken/clashed sets: 79
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497913 none O=C(COC1=CC=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 69, 120, 155, 201, 201, 201, 201, 201, 52, 52, 52, 52, 52, 43, 31, 43, 13, 1, 1, 1, 1, 1, 1, 1, 52, 120, 120, 201, 201, 201, 201, 69, 52, 52, 52, 52, 52, 31, 31, 1, 52, 52] 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, 42, 43])
total number of confs: 640
number of broken/clashed sets: 79
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497913 none O=C(COC1=CC=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 1, 1, 1, 1, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 13, 6, 1, 1, 1, 1, 1, 1, 1, 31, 31, 41, 41, 41, 41, 41, 52, 52, 95, 140, 201, 201, 201, 201, 201, 41, 13, 13, 1, 1, 1, 1, 31, 41, 41, 41, 41, 41, 95, 95, 201, 41, 41] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 579
number of broken/clashed sets: 79
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497913 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497913
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497913/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497913
Building REAL300025497914
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497914'
/scratch/stefan/7787277/working/building/REAL300025497914 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497914

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497914/0 /scratch/stefan/7787277/working/building/REAL300025497914 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 795)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/795
`/scratch/stefan/7787277/working/3D/795' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCOCC1)

`REAL300025497914.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497914.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497914/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497914 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 30, 99, 99, 99, 99, 99, 1, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 14, 14, 99, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 39, 20, 38, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 197
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497914 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 119, 119, 119, 99, 99, 99, 99, 99, 76, 48, 76, 12, 1, 1, 1, 1, 1, 1, 1, 99, 201, 201, 201, 201, 201, 201, 201, 201, 119, 99, 99, 99, 99, 99, 48, 48, 1, 99, 99, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 698
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497914 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCOCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 5, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 34, 34, 61, 105, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 1, 2, 2, 2, 3, 9, 9, 9, 9, 9, 61, 61, 201, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 40, 41, 42, 43, 44, 45, 46, 47, 21, 22, 23, 24, 25] set([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])
total number of confs: 468
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497914 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497914
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497914/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497914
Building REAL300025497915
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497915'
/scratch/stefan/7787277/working/building/REAL300025497915 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497915

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497915/0 /scratch/stefan/7787277/working/building/REAL300025497915 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 796)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/796
`/scratch/stefan/7787277/working/3D/796' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497915.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497915.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497915/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497915 none CC(C)CC(C)CC(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 201, 193, 201, 96, 96, 96, 69, 69, 69, 69, 69, 53, 28, 53, 13, 1, 1, 1, 1, 1, 1, 1, 69, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 193, 193, 96, 69, 69, 69, 69, 69, 28, 28, 1, 69, 69] 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])
total number of confs: 779
number of broken/clashed sets: 122
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497915 none CC(C)CC(C)CC(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [35, 36, 36, 34, 21, 34, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 19, 69, 69, 69, 69, 69, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 34, 34, 34, 34, 21, 21, 5, 1, 1, 1, 1, 1, 9, 9, 69, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49])
total number of confs: 270
number of broken/clashed sets: 122
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497915 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497915
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497915/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497915
Building REAL300025497916
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497916'
/scratch/stefan/7787277/working/building/REAL300025497916 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497916

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497916/0 /scratch/stefan/7787277/working/building/REAL300025497916 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 797)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/797
`/scratch/stefan/7787277/working/3D/797' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN3C=CN=C3C=C2)C1)

`REAL300025497916.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497916.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497916/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497916 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN3C=CN=C3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 5, 7, 7, 6, 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: [5, 1, 5, 15, 28, 83, 83, 83, 83, 83, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 1, 15, 15, 83, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 175
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497916 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN3C=CN=C3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 5, 7, 7, 6, 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: [37, 13, 37, 76, 114, 201, 201, 201, 201, 201, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 76, 76, 201, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 13, 13] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 504
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497916 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN3C=CN=C3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 1, 1, 5, 7, 7, 6, 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: [64, 46, 13, 1, 1, 1, 1, 1, 1, 1, 64, 83, 83, 83, 83, 83, 102, 102, 102, 201, 201, 201, 201, 201, 201, 201, 201, 83, 46, 46, 1, 83, 83, 83, 83, 83, 102, 201, 201, 201, 201, 201, 83, 83] 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: 480
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497916 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497916
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497916/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497916
Building REAL300025497917
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497917'
/scratch/stefan/7787277/working/building/REAL300025497917 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497917

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497917/0 /scratch/stefan/7787277/working/building/REAL300025497917 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 798)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/798
`/scratch/stefan/7787277/working/3D/798' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)(C)C)

`REAL300025497917.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497917.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497917/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497917 none CCC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 146, 146, 146, 114, 114, 114, 114, 114, 84, 31, 84, 13, 1, 1, 1, 1, 1, 1, 1, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 146, 114, 114, 114, 114, 114, 31, 31, 1, 114, 114, 201, 201, 201, 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, 53, 54])
total number of confs: 719
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: REAL300025497917 none CCC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 45, 114, 114, 114, 114, 114, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 1, 24, 24, 114, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10] 201
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 44, 40, 22, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49, 50, 51, 52, 53, 54])
total number of confs: 243
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497917 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497917
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497917/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497917
Building REAL300025497918
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497918'
/scratch/stefan/7787277/working/building/REAL300025497918 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497918

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497918/0 /scratch/stefan/7787277/working/building/REAL300025497918 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 799)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/799
`/scratch/stefan/7787277/working/3D/799' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC(F)(F)C1)

`REAL300025497918.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497918.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497918/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497918 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC(F)(F)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 15, 15, 5, 7, 7, 7, 6, 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]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 29, 91, 91, 91, 91, 91, 1, 15, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 14, 14, 91, 1, 1, 15, 15, 15, 15] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 39, 20, 38, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43])
total number of confs: 201
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497918 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC(F)(F)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 15, 15, 5, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 108, 108, 108, 91, 91, 91, 91, 91, 72, 47, 72, 13, 1, 1, 1, 1, 1, 1, 1, 91, 201, 201, 201, 201, 201, 201, 201, 201, 108, 91, 91, 91, 91, 91, 47, 47, 1, 91, 91, 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])
total number of confs: 653
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497918 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC(F)(F)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 15, 15, 5, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  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, 15, 15, 15, 15, 15, 39, 39, 72, 108, 201, 201, 201, 201, 201, 15, 1, 1, 1, 1, 1, 2, 2, 2, 7, 15, 15, 15, 15, 15, 72, 72, 201, 15, 15, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 40, 41, 42, 43, 21, 22, 23, 24, 25] set([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])
total number of confs: 507
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497918 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497918
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497918/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497918
Building REAL300025497919
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497919'
/scratch/stefan/7787277/working/building/REAL300025497919 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497919

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497919/0 /scratch/stefan/7787277/working/building/REAL300025497919 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 800)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/800
`/scratch/stefan/7787277/working/3D/800' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=C(CCC3)N2)C1)

`REAL300025497919.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497919.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497919/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497919 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=C(CCC3)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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, 32, 55, 148, 148, 148, 148, 148, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 1, 32, 32, 148, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 44, 10, 11, 12, 13, 14, 15, 45, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 307
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497919 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=C(CCC3)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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: [40, 15, 40, 94, 129, 201, 201, 201, 201, 201, 15, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 15, 94, 94, 201, 15, 15, 15, 15, 15, 4, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 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, 44, 45])
total number of confs: 536
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497919 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=C(CCC3)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 5, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock 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, 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: [106, 44, 13, 1, 1, 1, 1, 1, 1, 1, 106, 148, 148, 148, 148, 148, 194, 194, 194, 201, 201, 201, 201, 201, 201, 201, 147, 44, 44, 1, 148, 148, 148, 148, 148, 194, 201, 201, 201, 201, 201, 201, 201, 201, 148, 148] 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: 596
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497919 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497919
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497919/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497919
Building REAL300025497920
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497920'
/scratch/stefan/7787277/working/building/REAL300025497920 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497920

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497920/0 /scratch/stefan/7787277/working/building/REAL300025497920 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 801)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/801
`/scratch/stefan/7787277/working/3D/801' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(Cl)=N1)

`REAL300025497920.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497920.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497920/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497920 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 16, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 32, 93, 93, 93, 93, 93, 1, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 17, 17, 93, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 195
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497920 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 16, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 111, 111, 111, 93, 93, 93, 93, 93, 69, 41, 69, 12, 1, 1, 1, 1, 1, 1, 1, 93, 201, 201, 201, 201, 201, 201, 201, 111, 93, 93, 93, 93, 93, 41, 41, 1, 93, 93] 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])
total number of confs: 489
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497920 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(Cl)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'Cl', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 16, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 14, 14, 14, 14, 14, 35, 35, 65, 101, 201, 201, 201, 201, 201, 14, 1, 1, 1, 2, 2, 2, 1, 5, 14, 14, 14, 14, 14, 65, 65, 201, 14, 14] 201
rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 485
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497920 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497920
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497920/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497920
Building REAL300025497921
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497921'
/scratch/stefan/7787277/working/building/REAL300025497921 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497921

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497921/0 /scratch/stefan/7787277/working/building/REAL300025497921 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 802)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/802
`/scratch/stefan/7787277/working/3D/802' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1=NOC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497921.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497921.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497921/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497921 none COCC1=NOC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 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]
0  hydrogens 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, 24, 15, 15, 15, 15, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 15, 61, 61, 61, 61, 61, 1, 31, 31, 31, 24, 24, 15, 5, 1, 1, 1, 1, 1, 8, 8, 61, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 182
number of broken/clashed sets: 73
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497921 none COCC1=NOC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 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]
0  hydrogens need rotated
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, 172, 172, 172, 172, 98, 98, 98, 61, 61, 61, 61, 61, 45, 29, 45, 13, 1, 1, 1, 1, 1, 1, 1, 61, 201, 201, 201, 201, 201, 172, 98, 61, 61, 61, 61, 61, 29, 29, 1, 61, 61] 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, 42, 43])
total number of confs: 605
number of broken/clashed sets: 73
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497921 none COCC1=NOC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 5, 1, 8, 12, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 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]
0  hydrogens 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, 1, 5, 5, 5, 15, 15, 15, 15, 15, 27, 27, 53, 84, 172, 172, 172, 172, 172, 15, 12, 12, 12, 4, 4, 1, 5, 15, 15, 15, 15, 15, 53, 53, 172, 15, 15] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 418
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497921 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497921
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497921/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497921
Building REAL300025497922
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497922'
/scratch/stefan/7787277/working/building/REAL300025497922 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497922

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497922/0 /scratch/stefan/7787277/working/building/REAL300025497922 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 803)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/803
`/scratch/stefan/7787277/working/3D/803' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)N1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1)

`REAL300025497922.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497922.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497922/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497922 none CC(C)N1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [22, 13, 22, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 35, 83, 83, 83, 83, 83, 1, 13, 13, 22, 22, 22, 22, 22, 22, 22, 13, 5, 1, 1, 1, 1, 1, 19, 19, 83, 1, 1, 13] 201
rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46])
total number of confs: 235
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497922 none CC(C)N1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 101, 101, 101, 83, 83, 83, 83, 83, 68, 41, 68, 13, 1, 1, 1, 1, 1, 1, 1, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 83, 83, 83, 83, 83, 41, 41, 1, 83, 83, 201] 201
rigid atoms, others: [43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46])
total number of confs: 500
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497922 none CC(C)N1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [5, 1, 5, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 33, 33, 72, 115, 201, 201, 201, 201, 201, 13, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 5, 13, 13, 13, 13, 13, 72, 72, 201, 13, 13, 1] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 46, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 521
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497922 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497922
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497922/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497922
Building REAL300025497923
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497923'
/scratch/stefan/7787277/working/building/REAL300025497923 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497923

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497923/0 /scratch/stefan/7787277/working/building/REAL300025497923 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 804)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/804
`/scratch/stefan/7787277/working/3D/804' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C)C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1)

`REAL300025497923.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497923.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497923/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497923 none CCC1=C(C)C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 7, 7, 7, 7, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 35, 107, 107, 107, 107, 107, 1, 7, 22, 22, 22, 22, 22, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 19, 19, 107, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 275
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497923 none CCC1=C(C)C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 139, 139, 139, 139, 139, 139, 139, 139, 107, 107, 107, 107, 107, 84, 41, 84, 13, 1, 1, 1, 1, 1, 1, 1, 107, 139, 201, 201, 201, 201, 201, 139, 139, 139, 139, 139, 107, 107, 107, 107, 107, 41, 41, 1, 107, 107] 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])
total number of confs: 815
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497923 none CCC1=C(C)C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 4, 4, 4, 7, 7, 7, 7, 7, 18, 18, 39, 62, 139, 139, 139, 139, 139, 7, 1, 6, 6, 6, 5, 5, 2, 2, 2, 1, 4, 7, 7, 7, 7, 7, 39, 39, 139, 7, 7] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 35, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 327
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497923 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497923
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497923/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497923
Building REAL300025497924
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497924'
/scratch/stefan/7787277/working/building/REAL300025497924 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497924

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497924/0 /scratch/stefan/7787277/working/building/REAL300025497924 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 805)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/805
`/scratch/stefan/7787277/working/3D/805' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1C)

`REAL300025497924.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497924.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497924/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497924 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 6, 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, 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: [9, 9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 33, 56, 147, 147, 147, 147, 147, 1, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 33, 33, 147, 1, 1, 9, 9, 9] 201
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45])
total number of confs: 304
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497924 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 147, 147, 147, 147, 147, 103, 43, 103, 13, 1, 1, 1, 1, 1, 1, 1, 147, 201, 201, 201, 201, 201, 201, 201, 201, 201, 147, 147, 147, 147, 147, 43, 43, 1, 147, 147, 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])
total number of confs: 597
number of broken/clashed sets: 29
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497924 none CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1C NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 5, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 28, 28, 83, 118, 201, 201, 201, 201, 201, 9, 1, 1, 1, 2, 2, 2, 1, 1, 3, 9, 9, 9, 9, 9, 83, 83, 201, 9, 9, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 530
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497924 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497924
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497924/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497924
Building REAL300025497925
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497925'
/scratch/stefan/7787277/working/building/REAL300025497925 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497925

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497925/0 /scratch/stefan/7787277/working/building/REAL300025497925 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 806)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/806
`/scratch/stefan/7787277/working/3D/806' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=CN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497925.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497925.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497925/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497925 none CC1=CN=CN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 51, 27, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 10, 47, 47, 47, 47, 47, 1, 51, 51, 51, 51, 51, 27, 27, 5, 1, 1, 1, 1, 1, 6, 6, 47, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 207
number of broken/clashed sets: 64
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497925 none CC1=CN=CN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 156, 70, 70, 70, 47, 47, 47, 47, 47, 35, 26, 35, 12, 1, 1, 1, 1, 1, 1, 1, 47, 201, 201, 201, 201, 201, 156, 156, 70, 47, 47, 47, 47, 47, 26, 26, 1, 47, 47] 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])
total number of confs: 676
number of broken/clashed sets: 64
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497925 none CC1=CN=CN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 1, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 24, 24, 24, 51, 51, 51, 51, 51, 64, 64, 90, 128, 201, 201, 201, 201, 201, 51, 2, 2, 2, 1, 1, 6, 6, 24, 51, 51, 51, 51, 51, 90, 90, 201, 51, 51] 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: 544
number of broken/clashed sets: 64
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497925 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497925/1 /scratch/stefan/7787277/working/building/REAL300025497925 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 807)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/807
`/scratch/stefan/7787277/working/3D/807' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C[NH+]=CN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497925.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497925.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497925/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497925 none CC1=C[NH+]=CN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 6, 1, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
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, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 1, 5, 5, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 4, 4, 4, 1, 1] 6
rigid atoms, others: [35, 36, 37, 38, 39, 44, 10, 11, 12, 13, 14, 15, 16, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 29
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497925 none CC1=C[NH+]=CN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 6, 1, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
6  conformations in input
total number of sets (complete confs): 6
using default count positions algorithm for smaller data
unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 6, 6, 6, 6, 5, 4, 4, 4, 4, 4, 4, 4, 1, 4, 4] 6
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, 43, 44])
total number of confs: 15
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497925 none CC1=C[NH+]=CN1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 8, 6, 1, 8, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
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, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 5, 2, 2, 2, 1, 1, 3, 3, 4, 5, 5, 5, 5, 5, 6, 6, 6, 5, 5] 6
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: 30
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497925 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497925
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497925/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497925/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497925
Building REAL300025497926
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497926'
/scratch/stefan/7787277/working/building/REAL300025497926 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497926

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497926/0 /scratch/stefan/7787277/working/building/REAL300025497926 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 808)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/808
`/scratch/stefan/7787277/working/3D/808' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC(F)F)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497926.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497926.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497926/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497926 none O=C(CCC(F)F)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 15, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [77, 77, 77, 178, 199, 201, 201, 43, 43, 43, 43, 43, 43, 40, 43, 13, 1, 1, 1, 1, 1, 1, 1, 43, 178, 178, 201, 201, 201, 77, 43, 43, 43, 43, 43, 40, 40, 1, 43, 43] 201
rigid atoms, others: [37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
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: REAL300025497926 none O=C(CCC(F)F)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'F', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 15, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [5, 5, 5, 26, 33, 50, 50, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 10, 43, 43, 43, 43, 43, 1, 26, 26, 43, 43, 41, 5, 1, 1, 1, 1, 1, 7, 7, 43, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 7, 8, 9, 10, 11, 12, 13, 23, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 317
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497926 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497926
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497926/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497926
Building REAL300025497927
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497927'
/scratch/stefan/7787277/working/building/REAL300025497927 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497927

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497927/0 /scratch/stefan/7787277/working/building/REAL300025497927 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 809)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/809
`/scratch/stefan/7787277/working/3D/809' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=NOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497927.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497927.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497927/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497927 none CCOC1=NOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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]
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: [24, 13, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 54, 153, 153, 153, 153, 153, 1, 8, 24, 24, 24, 24, 24, 5, 1, 1, 1, 1, 1, 29, 29, 153, 1, 1, 8] 196
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497927 none CCOC1=NOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
196  conformations in input
total number of sets (complete confs): 196
using faster count positions algorithm for large data
unique positions, atoms: [196, 192, 186, 186, 186, 186, 186, 186, 186, 153, 153, 153, 153, 153, 112, 46, 112, 13, 1, 1, 1, 1, 1, 1, 1, 153, 186, 196, 196, 196, 196, 196, 186, 153, 153, 153, 153, 153, 46, 46, 1, 153, 153, 186] 196
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: 599
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497927 none CCOC1=NOC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 12, 1, 8, 12, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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]
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: [9, 4, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 8, 8, 8, 24, 24, 58, 91, 186, 186, 186, 186, 186, 8, 1, 10, 10, 10, 9, 9, 3, 8, 8, 8, 8, 8, 58, 58, 186, 8, 8, 1] 196
rigid atoms, others: [2, 3, 4, 5, 6, 7, 43, 26] set([0, 1, 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: 450
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497927 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497927
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497927/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497927
Building REAL300025497928
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497928'
/scratch/stefan/7787277/working/building/REAL300025497928 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497928

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497928/0 /scratch/stefan/7787277/working/building/REAL300025497928 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 810)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/810
`/scratch/stefan/7787277/working/3D/810' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC3(CC3)CC2)C1)

`REAL300025497928.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497928.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497928/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497928 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC3(CC3)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [5, 1, 5, 18, 32, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 1, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 1, 18, 18, 77, 1, 1, 1, 1, 1, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 49, 50, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 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])
total number of confs: 211
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497928 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC3(CC3)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [54, 21, 54, 96, 139, 201, 201, 201, 201, 201, 21, 21, 21, 21, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 21, 96, 96, 201, 21, 21, 21, 21, 21, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 201
rigid atoms, others: [16, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 49, 50])
total number of confs: 555
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497928 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCC3(CC3)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [65, 41, 13, 1, 1, 1, 1, 1, 1, 1, 65, 77, 77, 77, 77, 77, 104, 104, 104, 201, 201, 201, 201, 201, 201, 201, 77, 41, 41, 1, 77, 77, 77, 77, 77, 104, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 77, 77] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 642
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497928 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497928
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497928/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497928
Building REAL300025497929
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497929'
/scratch/stefan/7787277/working/building/REAL300025497929 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497929

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497929/0 /scratch/stefan/7787277/working/building/REAL300025497929 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 811)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/811
`/scratch/stefan/7787277/working/3D/811' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1)

`REAL300025497929.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497929.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497929/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497929 none COCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 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]
0  hydrogens 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, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 26, 92, 92, 92, 92, 92, 1, 12, 12, 12, 27, 27, 27, 15, 15, 5, 1, 1, 1, 1, 1, 13, 13, 92, 1, 1, 12, 12, 12, 12, 12, 12] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47])
total number of confs: 230
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497929 none COCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  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, 128, 128, 92, 92, 92, 92, 92, 64, 30, 64, 13, 1, 1, 1, 1, 1, 1, 1, 92, 201, 201, 201, 201, 201, 201, 201, 201, 128, 92, 92, 92, 92, 92, 30, 30, 1, 92, 92, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 661
number of broken/clashed sets: 66
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497929 none COCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [11, 5, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 22, 22, 57, 105, 201, 201, 201, 201, 201, 12, 1, 1, 1, 11, 11, 11, 5, 5, 5, 12, 12, 12, 12, 12, 57, 57, 201, 12, 12, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 3, 4, 42, 43, 44, 45, 46, 47, 23, 24, 25] set([0, 1, 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: 495
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497929 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497929
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497929/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497929
Building REAL300025497930
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497930'
/scratch/stefan/7787277/working/building/REAL300025497930 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497930

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497930/0 /scratch/stefan/7787277/working/building/REAL300025497930 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 812)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/812
`/scratch/stefan/7787277/working/3D/812' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CNC(=O)C=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497930.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497930.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497930/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497930 none O=C(CC1=CNC(=O)C=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 11, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 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: [5, 5, 5, 16, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 19, 37, 37, 37, 37, 37, 1, 16, 16, 29, 29, 29, 29, 5, 1, 1, 1, 1, 1, 14, 14, 37, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 169
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497930 none O=C(CC1=CNC(=O)C=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 11, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 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: [55, 55, 55, 120, 201, 201, 201, 201, 201, 201, 37, 37, 37, 37, 37, 36, 29, 36, 13, 1, 1, 1, 1, 1, 1, 1, 37, 120, 120, 201, 201, 201, 201, 55, 37, 37, 37, 37, 37, 29, 29, 1, 37, 37] 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, 42, 43])
total number of confs: 645
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497930 none O=C(CC1=CNC(=O)C=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 8, 1, 11, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 4, 7, 6, 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: [9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 29, 29, 29, 29, 29, 61, 61, 99, 133, 201, 201, 201, 201, 201, 29, 3, 3, 1, 1, 1, 1, 9, 29, 29, 29, 29, 29, 99, 99, 201, 29, 29] 201
rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 562
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497930 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497930
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497930/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497930
Building REAL300025497931
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497931'
/scratch/stefan/7787277/working/building/REAL300025497931 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497931

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497931/0 /scratch/stefan/7787277/working/building/REAL300025497931 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 813)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/813
`/scratch/stefan/7787277/working/3D/813' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(F)F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497931.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497931.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497931/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497931 none CC(CC(F)F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 1, 1, 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, 6, 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: [188, 83, 188, 201, 201, 201, 83, 83, 45, 45, 45, 45, 45, 45, 41, 45, 13, 1, 1, 1, 1, 1, 1, 1, 45, 188, 188, 188, 188, 201, 201, 201, 83, 45, 45, 45, 45, 45, 41, 41, 1, 45, 45] 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])
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: REAL300025497931 none CC(CC(F)F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 15, 15, 1, 11, 8, 5, 1, 1, 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, 6, 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: [24, 5, 24, 37, 52, 52, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 45, 45, 45, 45, 45, 1, 24, 24, 24, 24, 37, 37, 52, 5, 1, 1, 1, 1, 1, 6, 6, 45, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 307
number of broken/clashed sets: 0
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497931 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497931
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497931/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497931
Building REAL300025497932
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497932'
/scratch/stefan/7787277/working/building/REAL300025497932 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497932

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497932/0 /scratch/stefan/7787277/working/building/REAL300025497932 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 814)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/814
`/scratch/stefan/7787277/working/3D/814' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1)

`REAL300025497932.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497932.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497932/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497932 none CC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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]
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: [39, 23, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 8, 16, 16, 16, 16, 16, 1, 39, 39, 39, 39, 39, 23, 23, 6, 1, 1, 1, 1, 1, 7, 7, 16, 1, 1, 39, 39, 39, 39] 54
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 21, 39, 38, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43])
total number of confs: 177
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497932 none CC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [54, 49, 28, 28, 28, 16, 16, 16, 16, 16, 16, 16, 16, 10, 1, 1, 1, 1, 1, 1, 1, 16, 54, 54, 54, 54, 54, 49, 49, 28, 16, 16, 16, 16, 16, 16, 16, 1, 16, 16, 54, 54, 54, 54] 54
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 201
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497932 none CC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
54  conformations in input
total number of sets (complete confs): 54
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 7, 18, 18, 18, 39, 39, 39, 39, 39, 51, 51, 52, 52, 54, 54, 54, 54, 54, 39, 1, 1, 2, 2, 2, 7, 7, 18, 39, 39, 39, 39, 39, 52, 52, 54, 39, 39, 1, 1, 1, 1] 54
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: 182
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497932 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497932
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497932/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497932
Building REAL300025497933
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497933'
/scratch/stefan/7787277/working/building/REAL300025497933 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497933

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497933/0 /scratch/stefan/7787277/working/building/REAL300025497933 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 815)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/815
`/scratch/stefan/7787277/working/3D/815' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCC(CC)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497933.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497933.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497933/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497933 none CCCCC(CC)CC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens need rotated
201  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, 162, 183, 198, 78, 78, 78, 76, 76, 76, 76, 76, 63, 30, 63, 13, 1, 1, 1, 1, 1, 1, 1, 76, 201, 201, 201, 201, 201, 201, 201, 201, 201, 185, 198, 196, 198, 198, 198, 162, 162, 78, 76, 76, 76, 76, 76, 30, 30, 1, 76, 76] 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: 898
number of broken/clashed sets: 124
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497933 none CCCCC(CC)CC(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens 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, 34, 34, 24, 11, 23, 29, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 17, 76, 76, 76, 76, 76, 1, 36, 36, 36, 36, 36, 34, 34, 34, 34, 25, 29, 27, 29, 29, 29, 11, 11, 3, 1, 1, 1, 1, 1, 8, 8, 76, 1, 1] 201
rigid atoms, others: [16, 15, 10, 11, 12, 13, 46, 45, 48, 49, 14, 54, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52])
total number of confs: 314
number of broken/clashed sets: 124
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497933 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497933
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497933/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497933
Building REAL300025497934
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497934'
/scratch/stefan/7787277/working/building/REAL300025497934 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497934

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497934/0 /scratch/stefan/7787277/working/building/REAL300025497934 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 816)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/816
`/scratch/stefan/7787277/working/3D/816' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CNC(=O)C1)

`REAL300025497934.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497934.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497934/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497934 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CNC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.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', 'C.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, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 41, 107, 107, 107, 107, 107, 1, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 16, 16, 107, 1, 1, 10, 10, 10, 10, 10] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 39, 20, 38, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44])
total number of confs: 213
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497934 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CNC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.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', 'C.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, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 143, 143, 143, 107, 107, 107, 107, 107, 86, 45, 86, 13, 1, 1, 1, 1, 1, 1, 1, 107, 201, 201, 201, 201, 201, 201, 201, 201, 143, 107, 107, 107, 107, 107, 45, 45, 1, 107, 107, 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])
total number of confs: 661
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497934 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CNC(=O)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.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', 'C.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, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 8, 1, 11, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 5, 5, 5, 10, 10, 10, 10, 10, 27, 27, 60, 102, 201, 201, 201, 201, 201, 10, 1, 1, 1, 1, 1, 2, 2, 2, 5, 10, 10, 10, 10, 10, 60, 60, 201, 10, 10, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 40, 41, 42, 43, 44, 21, 22, 23, 24, 25] set([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])
total number of confs: 450
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497934 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497934
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497934/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497934
Building REAL300025497935
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497935'
/scratch/stefan/7787277/working/building/REAL300025497935 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497935

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497935/0 /scratch/stefan/7787277/working/building/REAL300025497935 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 817)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/817
`/scratch/stefan/7787277/working/3D/817' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC2CC2C1)

`REAL300025497935.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497935.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497935/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497935 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC2CC2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 26, 88, 88, 88, 88, 88, 1, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 12, 12, 88, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 39, 20, 38, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 171
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497935 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC2CC2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 132, 132, 132, 88, 88, 88, 88, 88, 77, 46, 77, 13, 1, 1, 1, 1, 1, 1, 1, 88, 201, 201, 201, 201, 201, 201, 201, 201, 132, 88, 88, 88, 88, 88, 46, 46, 1, 88, 88, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [37, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 687
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497935 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC2CC2C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 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, 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]
0  hydrogens need rotated
201  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, 10, 10, 10, 10, 10, 24, 24, 50, 95, 201, 201, 201, 201, 201, 10, 1, 1, 1, 1, 1, 2, 2, 2, 4, 10, 10, 10, 10, 10, 50, 50, 201, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 40, 41, 42, 43, 44, 45, 46, 47, 21, 22, 23, 24, 25] set([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])
total number of confs: 434
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497935 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497935
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497935/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497935
Building REAL300025497936
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497936'
/scratch/stefan/7787277/working/building/REAL300025497936 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497936

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497936/0 /scratch/stefan/7787277/working/building/REAL300025497936 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 818)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/818
`/scratch/stefan/7787277/working/3D/818' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(CCF)CC2)C1)

`REAL300025497936.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497936.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497936/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497936 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(CCF)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 5, 7, 7, 6, 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: [3, 1, 3, 9, 16, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 28, 29, 11, 11, 1, 9, 9, 60, 1, 1, 1, 1, 1, 5, 28, 28, 29, 29, 11, 11, 11, 11, 1, 1] 201
rigid atoms, others: [32, 1, 43, 10, 11, 12, 13, 14, 15, 42, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 212
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497936 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(CCF)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 5, 7, 7, 6, 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: [22, 11, 22, 40, 57, 138, 138, 138, 138, 138, 11, 11, 11, 11, 5, 5, 1, 5, 1, 1, 7, 11, 1, 1, 11, 40, 40, 138, 11, 11, 11, 11, 11, 5, 7, 7, 11, 11, 1, 1, 1, 1, 11, 11] 201
rigid atoms, others: [38, 39, 40, 41, 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, 42, 43])
total number of confs: 346
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497936 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(CCF)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 15, 5, 5, 5, 7, 7, 6, 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: [45, 34, 13, 1, 1, 1, 1, 1, 1, 1, 45, 60, 60, 60, 60, 60, 86, 86, 86, 138, 201, 201, 138, 138, 60, 34, 34, 1, 60, 60, 60, 60, 60, 86, 201, 201, 201, 201, 138, 138, 138, 138, 60, 60] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 850
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497936 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497936
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497936/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497936
Building REAL300025497937
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497937'
/scratch/stefan/7787277/working/building/REAL300025497937 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497937

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497937/0 /scratch/stefan/7787277/working/building/REAL300025497937 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 819)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/819
`/scratch/stefan/7787277/working/3D/819' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC(C)(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497937.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497937.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497937/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497937 none COCC(C)(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 152, 201, 201, 75, 75, 75, 71, 71, 71, 71, 71, 53, 30, 53, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 152, 152, 75, 71, 71, 71, 71, 71, 30, 30, 1, 71, 71] 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: 847
number of broken/clashed sets: 77
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497937 none COCC(C)(C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 12, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 19, 16, 8, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 16, 71, 71, 71, 71, 71, 1, 24, 24, 24, 19, 19, 16, 16, 16, 16, 16, 16, 8, 8, 5, 1, 1, 1, 1, 1, 8, 8, 71, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 194
number of broken/clashed sets: 77
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497937 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497937
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497937/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497937
Building REAL300025497938
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497938'
/scratch/stefan/7787277/working/building/REAL300025497938 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497938

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497938/0 /scratch/stefan/7787277/working/building/REAL300025497938 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 820)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/820
`/scratch/stefan/7787277/working/3D/820' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COCC(F)F)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497938.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497938.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497938/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497938 none O=C(COCC(F)F)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 15, 15, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 132, 173, 201, 201, 201, 42, 42, 42, 42, 42, 42, 30, 42, 13, 1, 1, 1, 1, 1, 1, 1, 42, 132, 132, 201, 201, 201, 47, 42, 42, 42, 42, 42, 30, 30, 1, 42, 42] 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])
total number of confs: 748
number of broken/clashed sets: 168
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497938 none O=C(COCC(F)F)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 5, 5, 15, 15, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 8, 16, 31, 39, 39, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 42, 42, 42, 42, 42, 1, 8, 8, 31, 31, 39, 3, 1, 1, 1, 1, 1, 5, 5, 42, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 214
number of broken/clashed sets: 168
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497938 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497938
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497938/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497938
Building REAL300025497939
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497939'
/scratch/stefan/7787277/working/building/REAL300025497939 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497939

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497939/0 /scratch/stefan/7787277/working/building/REAL300025497939 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 821)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/821
`/scratch/stefan/7787277/working/3D/821' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1)

`REAL300025497939.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497939.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497939/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497939 none NC(=O)C1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 6, 6, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 32, 79, 79, 79, 79, 79, 1, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 19, 19, 79, 1, 1, 16] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41])
total number of confs: 189
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497939 none NC(=O)C1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 6, 6, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 100, 100, 100, 79, 79, 79, 79, 79, 65, 37, 65, 13, 1, 1, 1, 1, 1, 1, 1, 79, 201, 201, 201, 201, 201, 100, 79, 79, 79, 79, 79, 37, 37, 1, 79, 79, 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])
total number of confs: 493
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497939 none NC(=O)C1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 6, 6, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 16, 41, 41, 87, 127, 201, 201, 201, 201, 201, 16, 1, 1, 2, 2, 1, 5, 16, 16, 16, 16, 16, 87, 87, 201, 16, 16, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 25, 26, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 540
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497939 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497939
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497939/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497939
Building REAL300025497940
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497940'
/scratch/stefan/7787277/working/building/REAL300025497940 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497940

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497940/0 /scratch/stefan/7787277/working/building/REAL300025497940 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 822)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/822
`/scratch/stefan/7787277/working/3D/822' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)N1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497940.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497940.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497940/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497940 none CC(C)N1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [15, 8, 15, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 41, 149, 149, 149, 149, 149, 1, 8, 15, 15, 15, 15, 15, 15, 15, 8, 5, 1, 1, 1, 1, 1, 23, 22, 149, 1, 1, 8] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46])
total number of confs: 309
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497940 none CC(C)N1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 149, 149, 149, 149, 149, 111, 42, 111, 13, 1, 1, 1, 1, 1, 1, 1, 149, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 149, 149, 149, 149, 42, 42, 1, 149, 149, 201] 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: 617
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497940 none CC(C)N1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [4, 1, 4, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 8, 27, 27, 63, 98, 201, 201, 201, 201, 201, 8, 1, 5, 5, 5, 4, 4, 4, 4, 1, 4, 8, 8, 8, 8, 8, 63, 63, 201, 8, 8, 1] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 7, 46, 26] set([0, 2, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 475
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497940 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497940
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497940/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497940
Building REAL300025497941
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497941'
/scratch/stefan/7787277/working/building/REAL300025497941 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497941

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497941/0 /scratch/stefan/7787277/working/building/REAL300025497941 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 823)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/823
`/scratch/stefan/7787277/working/3D/823' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CCC[NH+]2CCC3)C1)

`REAL300025497941.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497941.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497941/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497941 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CCC[NH+]2CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 7, 7, 6, 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, 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
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [5, 1, 6, 10, 16, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 10, 10, 41, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 50
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 49, 50, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 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: 87
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497941 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CCC[NH+]2CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 7, 7, 6, 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, 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
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [16, 7, 16, 23, 34, 50, 50, 50, 50, 50, 7, 7, 7, 7, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 50, 7, 7, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50
rigid atoms, others: [16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 49, 50])
total number of confs: 126
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497941 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CCC[NH+]2CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 9, 6, 5, 5, 5, 5, 7, 7, 6, 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, 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
50  conformations in input
total number of sets (complete confs): 50
using default count positions algorithm for smaller data
unique positions, atoms: [36, 23, 12, 1, 1, 1, 1, 1, 1, 1, 36, 41, 41, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 23, 23, 1, 41, 41, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41] 50
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 165
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497941 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497941
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497941/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497941
Building REAL300025497942
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497942'
/scratch/stefan/7787277/working/building/REAL300025497942 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497942

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497942/0 /scratch/stefan/7787277/working/building/REAL300025497942 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 824)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/824
`/scratch/stefan/7787277/working/3D/824' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN3N=CC=C23)C1)

`REAL300025497942.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497942.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497942/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497942 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN3N=CC=C23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 7, 7, 6, 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: [5, 1, 5, 12, 17, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 1, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 1, 12, 12, 61, 1, 1, 1, 1, 1, 5, 21, 21, 21, 21, 21, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 138
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497942 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN3N=CC=C23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 7, 7, 6, 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: [45, 21, 45, 83, 111, 201, 201, 201, 201, 201, 21, 21, 21, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 83, 83, 201, 21, 21, 21, 21, 21, 9, 1, 1, 1, 1, 1, 21, 21] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 521
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497942 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN3N=CC=C23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 5, 7, 7, 6, 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: [45, 33, 13, 1, 1, 1, 1, 1, 1, 1, 45, 61, 61, 61, 61, 61, 84, 84, 84, 201, 201, 201, 201, 201, 201, 201, 201, 61, 33, 33, 1, 61, 61, 61, 61, 61, 84, 201, 201, 201, 201, 201, 61, 61] 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: 442
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497942 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497942
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497942/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497942
Building REAL300025497943
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497943'
/scratch/stefan/7787277/working/building/REAL300025497943 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497943

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497943/0 /scratch/stefan/7787277/working/building/REAL300025497943 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 825)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/825
`/scratch/stefan/7787277/working/3D/825' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1)

`REAL300025497943.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497943.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497943/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497943 none CCOC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 12, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 15, 6, 6, 6, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 21, 88, 88, 88, 88, 88, 1, 6, 6, 28, 28, 28, 28, 28, 5, 1, 1, 1, 1, 1, 11, 11, 88, 1, 1, 6] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 228
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497943 none CCOC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 12, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 128, 128, 128, 128, 128, 128, 88, 88, 88, 88, 88, 65, 39, 65, 13, 1, 1, 1, 1, 1, 1, 1, 88, 128, 128, 201, 201, 201, 201, 201, 128, 88, 88, 88, 88, 88, 39, 39, 1, 88, 88, 128] 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: 583
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497943 none CCOC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 12, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 11, 11, 24, 40, 128, 128, 128, 128, 128, 6, 1, 1, 16, 16, 16, 15, 15, 2, 6, 6, 6, 6, 6, 24, 24, 128, 6, 6, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 43, 25, 26] set([0, 1, 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])
total number of confs: 294
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497943 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497943
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497943/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497943
Building REAL300025497944
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497944'
/scratch/stefan/7787277/working/building/REAL300025497944 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497944

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497944/0 /scratch/stefan/7787277/working/building/REAL300025497944 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 826)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/826
`/scratch/stefan/7787277/working/3D/826' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1)

`REAL300025497944.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497944.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497944/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497944 none CCCC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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: [28, 22, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 34, 95, 95, 95, 95, 95, 1, 5, 5, 28, 28, 28, 28, 28, 22, 22, 5, 1, 1, 1, 1, 1, 19, 19, 95, 1, 1, 5] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45])
total number of confs: 292
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497944 none CCCC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 116, 116, 116, 116, 116, 116, 95, 95, 95, 95, 95, 76, 37, 76, 13, 1, 1, 1, 1, 1, 1, 1, 95, 116, 116, 201, 201, 201, 201, 201, 201, 201, 116, 95, 95, 95, 95, 95, 37, 37, 1, 95, 95, 116] 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: 863
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497944 none CCCC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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: [13, 9, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 12, 12, 29, 48, 116, 116, 116, 116, 116, 5, 1, 1, 13, 13, 13, 13, 13, 9, 9, 1, 5, 5, 5, 5, 5, 29, 29, 116, 5, 5, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 34, 45, 25, 26] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 290
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497944 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497944
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497944/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497944
Building REAL300025497945
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497945'
/scratch/stefan/7787277/working/building/REAL300025497945 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497945

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497945/0 /scratch/stefan/7787277/working/building/REAL300025497945 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 827)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/827
`/scratch/stefan/7787277/working/3D/827' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1)

`REAL300025497945.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497945.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497945/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497945 none CCCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7]
0  hydrogens 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, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 24, 83, 83, 83, 83, 83, 1, 11, 12, 12, 34, 34, 34, 34, 34, 28, 28, 5, 1, 1, 1, 1, 1, 12, 12, 83, 1, 1, 12, 12] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46])
total number of confs: 277
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497945 none CCCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7]
0  hydrogens need rotated
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, 132, 132, 132, 83, 83, 83, 83, 83, 59, 30, 59, 13, 1, 1, 1, 1, 1, 1, 1, 83, 174, 174, 174, 201, 201, 201, 201, 201, 201, 201, 132, 83, 83, 83, 83, 83, 30, 30, 1, 83, 83, 174, 174] 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: 635
number of broken/clashed sets: 47
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497945 none CCCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CO1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 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, 7]
0  hydrogens 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, 3, 3, 3, 12, 12, 12, 12, 12, 21, 21, 38, 63, 174, 174, 174, 174, 174, 12, 1, 1, 1, 10, 10, 10, 10, 10, 6, 6, 3, 12, 12, 12, 12, 12, 38, 38, 174, 12, 12, 1, 1] 201
rigid atoms, others: [2, 3, 4, 5, 45, 46, 24, 25, 26] set([0, 1, 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: 381
number of broken/clashed sets: 47
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497945 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497945
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497945/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497945
Building REAL300025497946
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497946'
/scratch/stefan/7787277/working/building/REAL300025497946 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497946

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497946/0 /scratch/stefan/7787277/working/building/REAL300025497946 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 828)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/828
`/scratch/stefan/7787277/working/3D/828' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CCC(C)(C)C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497946.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497946.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497946/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497946 none CC(CCC(C)(C)C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens 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, 88, 167, 201, 201, 201, 201, 201, 88, 88, 46, 46, 46, 46, 46, 40, 26, 40, 12, 1, 1, 1, 1, 1, 1, 1, 46, 167, 167, 167, 167, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 88, 46, 46, 46, 46, 46, 26, 26, 1, 46, 46] 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: 846
number of broken/clashed sets: 60
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497946 none CC(CCC(C)(C)C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens 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, 18, 34, 34, 34, 34, 34, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 46, 46, 46, 46, 46, 1, 18, 18, 18, 18, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 5, 1, 1, 1, 1, 1, 6, 6, 46, 1, 1] 201
rigid atoms, others: [16, 15, 10, 11, 12, 13, 46, 45, 48, 49, 14, 54, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52])
total number of confs: 212
number of broken/clashed sets: 60
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497946 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497946
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497946/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497946
Building REAL300025497947
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497947'
/scratch/stefan/7787277/working/building/REAL300025497947 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497947

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497947/0 /scratch/stefan/7787277/working/building/REAL300025497947 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 829)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/829
`/scratch/stefan/7787277/working/3D/829' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCCCC(F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497947.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497947.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497947/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497947 none CCCCCCC(F)C(=O)NC1C=CCN(C(=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.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 5, 5, 15, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 149, 104, 149, 104, 104, 62, 62, 62, 62, 62, 51, 29, 51, 13, 1, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 104, 62, 62, 62, 62, 62, 29, 29, 1, 62, 62] 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, 50, 51])
total number of confs: 852
number of broken/clashed sets: 75
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497947 none CCCCCCC(F)C(=O)NC1C=CCN(C(=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.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 5, 5, 15, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 34, 32, 34, 32, 13, 5, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 62, 62, 62, 62, 62, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 13, 5, 1, 1, 1, 1, 1, 6, 6, 62, 1, 1] 201
rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 16, 50, 51, 46, 26, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49])
total number of confs: 262
number of broken/clashed sets: 75
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497947 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497947
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497947/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497947
Building REAL300025497948
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497948'
/scratch/stefan/7787277/working/building/REAL300025497948 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497948

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497948/0 /scratch/stefan/7787277/working/building/REAL300025497948 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 830)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/830
`/scratch/stefan/7787277/working/3D/830' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497948.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497948.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497948/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497948 none C[N@@H+]1CCC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 1, 1, 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, 6, 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]
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: [8, 8, 8, 8, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 8, 13, 13, 13, 13, 13, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 4, 1, 1, 1, 1, 1, 6, 6, 13, 1, 1, 8, 8] 15
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 48, 49])
total number of confs: 59
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497948 none C[N@@H+]1CCC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 1, 1, 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, 6, 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]
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, 13, 13, 13, 13, 13, 13, 12, 13, 10, 1, 1, 1, 1, 1, 1, 1, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13, 13, 13, 13, 12, 12, 1, 13, 13, 15, 15] 15
rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49])
total number of confs: 35
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497948 none C[N@@H+]1CCC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 1, 1, 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, 6, 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]
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, 4, 6, 6, 6, 8, 8, 8, 8, 8, 8, 8, 12, 12, 15, 15, 15, 15, 15, 8, 1, 2, 2, 2, 1, 1, 1, 1, 1, 4, 4, 6, 8, 8, 8, 8, 8, 12, 12, 15, 8, 8, 1, 1] 15
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 49, 48, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 56
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497948 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497948/1 /scratch/stefan/7787277/working/building/REAL300025497948 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 831)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/831
`/scratch/stefan/7787277/working/3D/831' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497948.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497948.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497948/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497948 none C[N@H+]1CCC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [8, 8, 8, 8, 8, 5, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 10, 19, 19, 19, 19, 19, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 4, 1, 1, 1, 1, 1, 6, 6, 19, 1, 1, 8, 8] 23
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 48, 49])
total number of confs: 66
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497948 none C[N@H+]1CCC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [23, 23, 23, 23, 23, 19, 19, 19, 19, 19, 19, 19, 19, 19, 18, 16, 18, 11, 1, 1, 1, 1, 1, 1, 1, 19, 23, 23, 23, 23, 23, 23, 23, 23, 23, 19, 19, 19, 19, 19, 19, 19, 19, 16, 16, 1, 19, 19, 23, 23] 23
rigid atoms, others: [45, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49])
total number of confs: 65
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497948 none C[N@H+]1CCC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
23  conformations in input
total number of sets (complete confs): 23
using default count positions algorithm for smaller data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 8, 8, 8, 8, 8, 9, 9, 19, 21, 23, 23, 23, 23, 23, 8, 1, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 5, 8, 8, 8, 8, 8, 19, 19, 23, 8, 8, 1, 1] 23
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 33, 49, 48, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 88
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497948 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497948
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497948/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497948/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497948
Building REAL300025497949
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497949'
/scratch/stefan/7787277/working/building/REAL300025497949 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497949

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497949/0 /scratch/stefan/7787277/working/building/REAL300025497949 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 832)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/832
`/scratch/stefan/7787277/working/3D/832' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NC=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497949.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497949.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497949/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497949 none CN1C=NC=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 26, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 26, 99, 99, 99, 99, 99, 1, 28, 28, 28, 28, 28, 26, 26, 5, 1, 1, 1, 1, 1, 16, 16, 99, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 254
number of broken/clashed sets: 57
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497949 none CN1C=NC=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 99, 99, 99, 99, 99, 52, 30, 52, 13, 1, 1, 1, 1, 1, 1, 1, 99, 201, 201, 201, 201, 201, 201, 201, 126, 99, 99, 99, 99, 99, 30, 30, 1, 99, 99] 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])
total number of confs: 728
number of broken/clashed sets: 57
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497949 none CN1C=NC=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 13, 13, 13, 28, 28, 28, 28, 28, 56, 56, 89, 122, 201, 201, 201, 201, 201, 28, 2, 2, 2, 1, 1, 3, 3, 13, 28, 28, 28, 28, 28, 89, 89, 201, 28, 28] 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: 542
number of broken/clashed sets: 57
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497949 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497949
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497949/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497949
Building REAL300025497950
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497950'
/scratch/stefan/7787277/working/building/REAL300025497950 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497950

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497950/0 /scratch/stefan/7787277/working/building/REAL300025497950 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 833)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/833
`/scratch/stefan/7787277/working/3D/833' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3NC=CC=C3N=C2)C1)

`REAL300025497950.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497950.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497950/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497950 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3NC=CC=C3N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 19, 38, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 1, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 22, 1, 19, 19, 105, 1, 1, 1, 1, 1, 5, 22, 22, 22, 22, 22, 1, 1] 184
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 225
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497950 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3NC=CC=C3N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [38, 22, 38, 85, 119, 184, 184, 184, 184, 184, 22, 22, 22, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 85, 85, 184, 22, 22, 22, 22, 22, 9, 1, 1, 1, 1, 1, 22, 22] 184
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 488
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497950 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3NC=CC=C3N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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
184  conformations in input
total number of sets (complete confs): 184
using faster count positions algorithm for large data
unique positions, atoms: [94, 42, 13, 1, 1, 1, 1, 1, 1, 1, 94, 105, 105, 105, 105, 105, 130, 130, 130, 184, 184, 184, 184, 184, 184, 184, 184, 105, 42, 42, 1, 105, 105, 105, 105, 105, 130, 184, 184, 184, 184, 184, 105, 105] 184
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: 508
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497950 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497950
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497950/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497950
Building REAL300025497951
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497951'
/scratch/stefan/7787277/working/building/REAL300025497951 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497951

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497951/0 /scratch/stefan/7787277/working/building/REAL300025497951 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 834)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/834
`/scratch/stefan/7787277/working/3D/834' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(COC1=CSC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497951.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497951.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497951/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497951 none O=C(COC1=CSC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 1, 1, 14, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 9, 21, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 12, 53, 53, 53, 53, 53, 1, 9, 9, 40, 40, 40, 4, 1, 1, 1, 1, 1, 6, 6, 53, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 159
number of broken/clashed sets: 80
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497951 none O=C(COC1=CSC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 1, 1, 14, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 104, 139, 201, 201, 201, 201, 53, 53, 53, 53, 53, 43, 27, 43, 13, 1, 1, 1, 1, 1, 1, 1, 53, 104, 104, 201, 201, 201, 61, 53, 53, 53, 53, 53, 27, 27, 1, 53, 53] 201
rigid atoms, others: [39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41])
total number of confs: 593
number of broken/clashed sets: 80
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497951 none O=C(COC1=CSC=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 12, 1, 1, 14, 1, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 15, 6, 1, 1, 1, 1, 1, 1, 33, 33, 40, 40, 40, 40, 40, 48, 48, 88, 128, 201, 201, 201, 201, 201, 40, 15, 15, 1, 1, 1, 33, 40, 40, 40, 40, 40, 88, 88, 201, 40, 40] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 28, 29, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 548
number of broken/clashed sets: 80
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497951 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497951
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497951/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497951
Building REAL300025497952
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497952'
/scratch/stefan/7787277/working/building/REAL300025497952 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497952

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497952/0 /scratch/stefan/7787277/working/building/REAL300025497952 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 835)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/835
`/scratch/stefan/7787277/working/3D/835' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1)

`REAL300025497952.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497952.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497952/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497952 none CCC1=CC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', '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, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 12, 12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 28, 88, 88, 88, 88, 88, 1, 12, 26, 26, 26, 26, 26, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 16, 16, 88, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 258
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497952 none CCC1=CC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', '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, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 98, 98, 98, 88, 88, 88, 88, 88, 71, 40, 71, 13, 1, 1, 1, 1, 1, 1, 1, 88, 130, 201, 201, 201, 201, 201, 130, 130, 130, 130, 98, 88, 88, 88, 88, 88, 40, 40, 1, 88, 88] 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])
total number of confs: 800
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497952 none CCC1=CC(C)=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', '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, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 12, 12, 12, 12, 12, 25, 25, 46, 71, 130, 130, 130, 130, 130, 12, 1, 5, 6, 6, 5, 5, 1, 2, 2, 2, 3, 12, 12, 12, 12, 12, 46, 46, 130, 12, 12] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 344
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497952 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497952
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497952/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497952
Building REAL300025497953
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497953'
/scratch/stefan/7787277/working/building/REAL300025497953 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497953

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497953/0 /scratch/stefan/7787277/working/building/REAL300025497953 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 836)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/836
`/scratch/stefan/7787277/working/3D/836' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497953.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497953.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497953/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497953 none CCN1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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: [13, 7, 7, 7, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 34, 85, 85, 85, 85, 85, 1, 7, 13, 13, 13, 13, 13, 7, 5, 1, 1, 1, 1, 1, 20, 20, 85, 1, 1, 7] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 225
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497953 none CCN1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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, 102, 102, 102, 102, 102, 102, 102, 85, 85, 85, 85, 85, 72, 37, 72, 13, 1, 1, 1, 1, 1, 1, 1, 85, 102, 201, 201, 201, 201, 201, 102, 102, 85, 85, 85, 85, 85, 37, 37, 1, 85, 85, 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: 927
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497953 none CCN1C=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 8, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 6, 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: [3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 19, 19, 40, 57, 102, 102, 102, 102, 102, 7, 1, 3, 3, 3, 3, 3, 1, 3, 7, 7, 7, 7, 7, 40, 40, 102, 7, 7, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 43, 25, 31] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 263
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497953 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497953
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497953/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497953
Building REAL300025497954
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497954'
/scratch/stefan/7787277/working/building/REAL300025497954 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497954

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497954/0 /scratch/stefan/7787277/working/building/REAL300025497954 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 837)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/837
`/scratch/stefan/7787277/working/3D/837' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CO1)

`REAL300025497954.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497954.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497954/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497954 none CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.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', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 125, 125, 125, 75, 75, 75, 75, 75, 58, 30, 58, 13, 1, 1, 1, 1, 1, 1, 1, 75, 201, 201, 201, 201, 201, 201, 201, 201, 201, 200, 200, 125, 75, 75, 75, 75, 75, 30, 30, 1, 75, 75, 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])
total number of confs: 768
number of broken/clashed sets: 82
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497954 none CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.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', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 24, 24, 24, 34, 34, 34, 34, 34, 44, 44, 89, 138, 201, 201, 201, 201, 201, 34, 1, 1, 1, 1, 1, 6, 6, 6, 5, 13, 13, 24, 34, 34, 34, 34, 34, 89, 89, 201, 34, 34, 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: 570
number of broken/clashed sets: 82
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497954 none CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.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', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 12, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 15, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 17, 75, 75, 75, 75, 75, 1, 22, 34, 34, 34, 34, 22, 22, 22, 22, 15, 15, 4, 1, 1, 1, 1, 1, 8, 8, 75, 1, 1, 34, 34, 34] 201
rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 43, 21, 38, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46])
total number of confs: 227
number of broken/clashed sets: 82
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497954 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497954
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497954/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497954
Building REAL300025497955
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497955'
/scratch/stefan/7787277/working/building/REAL300025497955 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497955

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497955/0 /scratch/stefan/7787277/working/building/REAL300025497955 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 838)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/838
`/scratch/stefan/7787277/working/3D/838' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C)

`REAL300025497955.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497955.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497955/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497955 none CCC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [69, 69, 46, 46, 46, 23, 23, 23, 23, 23, 23, 19, 23, 11, 1, 1, 1, 1, 1, 1, 1, 23, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 46, 23, 23, 23, 23, 23, 19, 19, 1, 23, 23, 69, 69, 69, 69, 69, 69] 69
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])
total number of confs: 257
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: REAL300025497955 none CCC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 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]
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: [23, 22, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 10, 23, 23, 23, 23, 23, 1, 22, 25, 25, 25, 25, 25, 25, 25, 25, 22, 6, 1, 1, 1, 1, 1, 8, 8, 23, 1, 1, 25, 25, 25, 25, 25, 25] 69
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 41, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48])
total number of confs: 171
number of broken/clashed sets: 54
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497955 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497955
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497955/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497955
Building REAL300025497956
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497956'
/scratch/stefan/7787277/working/building/REAL300025497956 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497956

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497956/0 /scratch/stefan/7787277/working/building/REAL300025497956 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 839)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/839
`/scratch/stefan/7787277/working/3D/839' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CC=C1)

`REAL300025497956.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497956.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497956/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497956 none C[C@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 154, 201, 154, 154, 100, 100, 100, 100, 100, 80, 39, 80, 13, 1, 1, 1, 1, 1, 1, 1, 100, 201, 201, 201, 201, 201, 201, 201, 201, 201, 154, 100, 100, 100, 100, 100, 39, 39, 1, 100, 100, 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])
total number of confs: 741
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497956 none C[C@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 8, 8, 8, 17, 17, 17, 17, 17, 43, 43, 87, 129, 201, 201, 201, 201, 201, 17, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 17, 17, 17, 17, 17, 87, 87, 201, 17, 17, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 42, 43, 44, 45, 46, 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])
total number of confs: 541
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497956 none C[C@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 5, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 34, 100, 100, 100, 100, 100, 1, 14, 17, 17, 14, 17, 17, 14, 14, 14, 5, 1, 1, 1, 1, 1, 20, 20, 100, 1, 1, 17, 17, 14, 17, 17] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 41] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46])
total number of confs: 253
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497956 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497956
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497956/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497956
Building REAL300025497957
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497957'
/scratch/stefan/7787277/working/building/REAL300025497957 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497957

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497957/0 /scratch/stefan/7787277/working/building/REAL300025497957 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 840)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/840
`/scratch/stefan/7787277/working/3D/840' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN(C)C(=O)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497957.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497957.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497957/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497957 none CN(C)C(=O)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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, 201, 201, 199, 201, 196, 180, 110, 110, 110, 77, 77, 77, 77, 77, 56, 29, 56, 13, 1, 1, 1, 1, 1, 1, 1, 77, 201, 201, 201, 201, 201, 201, 199, 199, 199, 199, 180, 180, 110, 77, 77, 77, 77, 77, 29, 29, 1, 77, 77] 201
rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49])
total number of confs: 823
number of broken/clashed sets: 73
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497957 none CN(C)C(=O)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 8, 5, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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: [29, 29, 29, 23, 29, 21, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 17, 77, 77, 77, 77, 77, 1, 29, 29, 29, 29, 29, 29, 23, 23, 23, 23, 16, 16, 5, 1, 1, 1, 1, 1, 9, 9, 77, 1, 1] 201
rigid atoms, others: [48, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 249
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497957 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497957
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497957/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497957
Building REAL300025497958
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497958'
/scratch/stefan/7787277/working/building/REAL300025497958 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497958

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497958/0 /scratch/stefan/7787277/working/building/REAL300025497958 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 841)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/841
`/scratch/stefan/7787277/working/3D/841' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCNC(=O)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497958.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497958.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497958/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497958 none CCNC(=O)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['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.2', 'C.2', 'C.3', '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, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 142, 142, 134, 142, 112, 102, 47, 47, 47, 38, 38, 38, 38, 38, 38, 26, 38, 13, 1, 1, 1, 1, 1, 1, 1, 38, 201, 201, 201, 201, 201, 142, 129, 134, 117, 117, 102, 102, 47, 38, 38, 38, 38, 38, 26, 26, 1, 38, 38] 201
rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49])
total number of confs: 975
number of broken/clashed sets: 180
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497958 none CCNC(=O)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['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.2', 'C.2', 'C.3', '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, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [47, 28, 28, 20, 28, 14, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 9, 38, 38, 38, 38, 38, 1, 47, 47, 47, 47, 47, 28, 19, 20, 15, 15, 11, 11, 3, 1, 1, 1, 1, 1, 6, 6, 38, 1, 1] 201
rigid atoms, others: [48, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 280
number of broken/clashed sets: 180
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497958 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497958
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497958/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497958
Building REAL300025497959
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497959'
/scratch/stefan/7787277/working/building/REAL300025497959 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497959

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497959/0 /scratch/stefan/7787277/working/building/REAL300025497959 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 842)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/842
`/scratch/stefan/7787277/working/3D/842' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCNC(=O)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497959.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497959.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497959/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497959 none CCCNC(=O)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
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, 159, 127, 159, 127, 73, 73, 73, 68, 68, 68, 68, 68, 57, 31, 57, 13, 1, 1, 1, 1, 1, 1, 1, 68, 201, 201, 201, 201, 201, 201, 201, 159, 127, 127, 127, 127, 73, 68, 68, 68, 68, 68, 31, 31, 1, 68, 68] 201
rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49])
total number of confs: 842
number of broken/clashed sets: 152
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497959 none CCCNC(=O)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 8, 1, 11, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens 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, 33, 14, 14, 9, 14, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 19, 68, 68, 68, 68, 68, 1, 45, 45, 45, 45, 45, 33, 33, 14, 9, 9, 9, 9, 3, 1, 1, 1, 1, 1, 11, 11, 68, 1, 1] 201
rigid atoms, others: [48, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 328
number of broken/clashed sets: 152
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497959 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497959
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497959/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497959
Building REAL300025497960
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497960'
/scratch/stefan/7787277/working/building/REAL300025497960 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497960

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497960/0 /scratch/stefan/7787277/working/building/REAL300025497960 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 843)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/843
`/scratch/stefan/7787277/working/3D/843' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CN=C1)

`REAL300025497960.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497960.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497960/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497960 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 110, 110, 110, 86, 86, 86, 86, 86, 53, 30, 53, 13, 1, 1, 1, 1, 1, 1, 1, 86, 132, 201, 201, 201, 201, 201, 132, 132, 132, 132, 110, 86, 86, 86, 86, 86, 30, 30, 1, 86, 86, 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])
total number of confs: 586
number of broken/clashed sets: 46
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497960 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 11, 11, 20, 20, 20, 20, 20, 42, 42, 74, 113, 201, 201, 201, 201, 201, 20, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 20, 20, 20, 20, 20, 74, 74, 201, 20, 20, 1, 1, 1, 1] 201
rigid atoms, others: [1, 42, 43, 44, 45, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 508
number of broken/clashed sets: 46
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497960 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 23, 86, 86, 86, 86, 86, 1, 10, 20, 20, 20, 20, 20, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 13, 13, 86, 1, 1, 20, 20, 20, 20] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 40, 20, 41, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45])
total number of confs: 198
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497960 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497960
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497960/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497960
Building REAL300025497961
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497961'
/scratch/stefan/7787277/working/building/REAL300025497961 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497961

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497961/0 /scratch/stefan/7787277/working/building/REAL300025497961 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 844)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/844
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2CCNC(=O)CC2)C1)

`REAL300025497961.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497961.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497961/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497961 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCNC(=O)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 7, 17, 32, 95, 94, 95, 95, 95, 1, 1, 1, 1, 1, 1, 4, 4, 4, 18, 18, 18, 18, 18, 18, 18, 1, 18, 18, 95, 1, 1, 1, 1, 1, 4, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 46, 26, 47, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 219
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497961 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCNC(=O)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 18, 45, 85, 119, 201, 201, 201, 201, 201, 18, 18, 18, 18, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 18, 85, 85, 201, 18, 18, 18, 18, 18, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 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, 46, 47])
total number of confs: 519
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497961 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCNC(=O)CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [72, 34, 13, 1, 1, 1, 1, 1, 1, 1, 72, 95, 95, 95, 95, 95, 134, 134, 134, 201, 201, 201, 201, 201, 201, 201, 95, 34, 34, 1, 95, 95, 95, 95, 95, 134, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 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, 44, 45, 46, 47])
total number of confs: 641
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497961 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497961
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497961/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497961
Building REAL300025497962
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497962'
/scratch/stefan/7787277/working/building/REAL300025497962 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497962

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497962/0 /scratch/stefan/7787277/working/building/REAL300025497962 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 845)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/845
`/scratch/stefan/7787277/working/3D/845' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3CCCC3=CO2)C1)

`REAL300025497962.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497962.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497962/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497962 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3CCCC3=CO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 12, 5, 7, 7, 6, 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, 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, 19, 43, 145, 145, 145, 145, 145, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 1, 19, 19, 145, 1, 1, 1, 1, 1, 5, 10, 10, 10, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 44, 10, 11, 12, 13, 14, 15, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 260
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497962 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3CCCC3=CO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 12, 5, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [31, 10, 31, 65, 107, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 10, 65, 65, 201, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 16, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44])
total number of confs: 459
number of broken/clashed sets: 29
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497962 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3CCCC3=CO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 5, 5, 5, 1, 1, 12, 5, 7, 7, 6, 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, 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: [109, 44, 13, 1, 1, 1, 1, 1, 1, 1, 109, 145, 145, 145, 145, 145, 200, 200, 200, 201, 201, 201, 201, 201, 201, 201, 145, 44, 44, 1, 145, 145, 145, 145, 145, 200, 201, 201, 201, 201, 201, 201, 201, 145, 145] 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: 610
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497962 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497962
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497962/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497962
Building REAL300025497963
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497963'
/scratch/stefan/7787277/working/building/REAL300025497963 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497963

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497963/0 /scratch/stefan/7787277/working/building/REAL300025497963 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 846)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/846
`/scratch/stefan/7787277/working/3D/846' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497963.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497963.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497963/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497963 none CC1=CN=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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: [30, 30, 30, 30, 30, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 20, 40, 40, 40, 40, 40, 1, 30, 30, 30, 30, 30, 30, 15, 15, 5, 1, 1, 1, 1, 1, 14, 14, 40, 1, 1, 30] 201
rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45])
total number of confs: 170
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497963 none CC1=CN=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 128, 55, 55, 55, 40, 40, 40, 40, 40, 38, 28, 38, 13, 1, 1, 1, 1, 1, 1, 1, 40, 201, 201, 201, 201, 201, 201, 128, 128, 55, 40, 40, 40, 40, 40, 28, 28, 1, 40, 40, 201] 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: 658
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497963 none CC1=CN=CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 11, 11, 11, 30, 30, 30, 30, 30, 57, 57, 97, 130, 201, 201, 201, 201, 201, 30, 1, 2, 2, 2, 1, 1, 4, 4, 11, 30, 30, 30, 30, 30, 97, 97, 201, 30, 30, 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: 579
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497963 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497963
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497963/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497963
Building REAL300025497964
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497964'
/scratch/stefan/7787277/working/building/REAL300025497964 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497964

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497964/0 /scratch/stefan/7787277/working/building/REAL300025497964 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 847)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/847
`/scratch/stefan/7787277/working/3D/847' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(C)(CCOC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497964.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497964.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497964/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497964 none C=CC(C)(CCOC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [1, 1, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need 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, 133, 196, 196, 197, 197, 201, 133, 133, 74, 74, 74, 74, 74, 54, 34, 54, 13, 1, 1, 1, 1, 1, 1, 1, 74, 201, 201, 201, 196, 196, 196, 197, 197, 197, 197, 201, 201, 201, 133, 74, 74, 74, 74, 74, 34, 34, 1, 74, 74] 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, 50])
total number of confs: 814
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: REAL300025497964 none C=CC(C)(CCOC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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: [1, 1, 5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens 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, 10, 10, 12, 12, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 18, 74, 74, 74, 74, 74, 1, 18, 18, 18, 10, 10, 10, 12, 12, 12, 12, 18, 18, 18, 5, 1, 1, 1, 1, 1, 9, 9, 74, 1, 1] 201
rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48])
total number of confs: 202
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497964 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497964
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497964/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497964
Building REAL300025497965
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497965'
/scratch/stefan/7787277/working/building/REAL300025497965 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497965

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497965/0 /scratch/stefan/7787277/working/building/REAL300025497965 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 848)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/848
`/scratch/stefan/7787277/working/3D/848' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCOC1)

`REAL300025497965.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497965.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497965/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497965 none COC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 7, 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, 3, 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: [159, 159, 154, 154, 154, 97, 97, 97, 97, 97, 67, 36, 67, 13, 1, 1, 1, 1, 1, 1, 1, 97, 159, 201, 201, 201, 201, 159, 159, 159, 159, 154, 97, 97, 97, 97, 97, 36, 36, 1, 97, 97, 201, 201, 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, 48])
total number of confs: 671
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497965 none COC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 7, 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, 3, 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: [6, 6, 1, 6, 7, 7, 7, 20, 20, 20, 20, 20, 36, 36, 66, 99, 201, 201, 201, 201, 201, 20, 1, 1, 1, 1, 1, 6, 6, 6, 6, 7, 20, 20, 20, 20, 20, 66, 66, 201, 20, 20, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 42, 43, 44, 45, 46, 47, 48, 22, 23, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 475
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497965 none COC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 12, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 12, 5, 7, 7, 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, 3, 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: [8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 21, 97, 97, 97, 97, 97, 1, 8, 20, 20, 20, 20, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 10, 10, 97, 1, 1, 20, 20, 20, 20, 20, 20, 20] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 41] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 209
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497965 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497965
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497965/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497965
Building REAL300025497966
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497966'
/scratch/stefan/7787277/working/building/REAL300025497966 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497966

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497966/0 /scratch/stefan/7787277/working/building/REAL300025497966 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 849)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/849
`/scratch/stefan/7787277/working/3D/849' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCOC1)

`REAL300025497966.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497966.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497966/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497966 none COCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [20, 13, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 34, 118, 118, 118, 118, 118, 1, 9, 9, 9, 9, 20, 20, 20, 13, 13, 5, 1, 1, 1, 1, 1, 17, 17, 118, 1, 1, 9, 9, 9, 9, 9, 9] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48])
total number of confs: 262
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497966 none COCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 139, 139, 139, 118, 118, 118, 118, 118, 67, 30, 67, 13, 1, 1, 1, 1, 1, 1, 1, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 139, 118, 118, 118, 118, 118, 30, 30, 1, 118, 118, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 624
number of broken/clashed sets: 49
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497966 none COCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 3, 7, 7, 7, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 4, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 26, 26, 59, 105, 201, 201, 201, 201, 201, 9, 1, 1, 1, 1, 8, 8, 8, 4, 4, 3, 9, 9, 9, 9, 9, 59, 59, 201, 9, 9, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 3, 4, 43, 44, 45, 46, 47, 48, 23, 24, 25, 26] set([0, 1, 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: 484
number of broken/clashed sets: 49
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497966 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497966
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497966/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497966
Building REAL300025497967
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497967'
/scratch/stefan/7787277/working/building/REAL300025497967 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497967

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497967/0 /scratch/stefan/7787277/working/building/REAL300025497967 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 850)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/850
`/scratch/stefan/7787277/working/3D/850' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C3CC3)CCC2)C1)

`REAL300025497967.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497967.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497967/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025497967 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C3CC3)CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 13, 22, 88, 88, 88, 88, 88, 1, 1, 1, 1, 1, 1, 5, 5, 5, 11, 28, 28, 11, 11, 11, 1, 13, 13, 88, 1, 1, 1, 1, 1, 5, 28, 28, 28, 28, 28, 11, 11, 11, 11, 11, 11, 1, 1] 201
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 14, 15, 46, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 224
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL300025497967 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C3CC3)CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 28, 45, 68, 101, 201, 201, 201, 201, 201, 28, 28, 28, 28, 12, 12, 8, 12, 1, 1, 1, 1, 8, 8, 8, 28, 68, 68, 201, 28, 28, 28, 28, 28, 12, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 28, 28] 201
rigid atoms, others: [35, 36, 37, 38, 39, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 474
number of broken/clashed sets: 67
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497967 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C3CC3)CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 11, 27, 47, 72, 172, 172, 172, 172, 172, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 8, 8, 1, 1, 1, 11, 47, 47, 172, 11, 11, 11, 11, 11, 4, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 11, 11] 201
rigid atoms, others: [40, 41, 42, 43, 44, 45, 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, 46, 47])
total number of confs: 388
number of broken/clashed sets: 67
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497967 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C3CC3)CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 36, 12, 1, 1, 1, 1, 1, 1, 1, 68, 88, 88, 88, 88, 88, 128, 128, 128, 172, 201, 201, 172, 172, 172, 88, 36, 36, 1, 88, 88, 88, 88, 88, 128, 201, 201, 201, 201, 201, 172, 172, 172, 172, 172, 172, 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, 45, 46, 47])
total number of confs: 663
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497967 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497967
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497967/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497967
Building REAL300025497968
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497968'
/scratch/stefan/7787277/working/building/REAL300025497968 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497968

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497968/0 /scratch/stefan/7787277/working/building/REAL300025497968 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 851)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/851
`/scratch/stefan/7787277/working/3D/851' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1)

`REAL300025497968.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497968.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497968/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497968 none CC(C)(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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: [165, 50, 165, 50, 50, 42, 42, 42, 42, 42, 25, 20, 25, 11, 1, 1, 1, 1, 1, 1, 1, 42, 165, 201, 201, 201, 165, 165, 165, 165, 165, 165, 50, 42, 42, 42, 42, 42, 20, 20, 1, 42, 42, 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])
total number of confs: 745
number of broken/clashed sets: 162
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497968 none CC(C)(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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: [7, 1, 7, 7, 9, 9, 9, 21, 21, 21, 21, 21, 47, 47, 83, 123, 201, 201, 201, 201, 201, 21, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 9, 21, 21, 21, 21, 21, 83, 83, 201, 21, 21, 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: 542
number of broken/clashed sets: 162
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497968 none CC(C)(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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, 5, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 11, 19, 42, 42, 42, 42, 42, 1, 16, 21, 21, 21, 16, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 11, 11, 42, 1, 1, 21, 21, 21, 21, 21, 21, 21] 201
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 41, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 163
number of broken/clashed sets: 162
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497968 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497968
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497968/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497968
Building REAL300025497969
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497969'
/scratch/stefan/7787277/working/building/REAL300025497969 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497969

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497969/0 /scratch/stefan/7787277/working/building/REAL300025497969 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 852)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/852
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2(C3CCC3)CCC2)C1)

`REAL300025497969.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497969.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497969/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025497969 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C3CCC3)CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [5, 1, 5, 16, 31, 128, 128, 128, 128, 128, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 15, 15, 15, 10, 10, 10, 1, 16, 16, 128, 1, 1, 1, 1, 1, 6, 15, 15, 15, 15, 15, 15, 15, 10, 10, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 49, 50, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 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])
total number of confs: 248
number of broken/clashed sets: 42
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.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: REAL300025497969 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C3CCC3)CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [32, 15, 32, 66, 105, 201, 201, 201, 201, 201, 15, 15, 15, 15, 7, 7, 4, 7, 1, 1, 1, 1, 1, 4, 4, 4, 15, 66, 66, 201, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 15, 15] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 472
number of broken/clashed sets: 42
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497969 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C3CCC3)CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [27, 10, 27, 62, 101, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 4, 4, 4, 1, 1, 1, 10, 62, 62, 201, 10, 10, 10, 10, 10, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [48, 43, 44, 45, 46, 47, 16, 18, 19, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 49, 50])
total number of confs: 465
number of broken/clashed sets: 42
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497969 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C3CCC3)CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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: [90, 38, 13, 1, 1, 1, 1, 1, 1, 1, 90, 128, 128, 128, 128, 128, 175, 175, 175, 201, 201, 201, 201, 201, 201, 201, 128, 38, 38, 1, 128, 128, 128, 128, 128, 175, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 128] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 629
number of broken/clashed sets: 42
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497969 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497969
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497969/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497969
Building REAL300025497970
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497970'
/scratch/stefan/7787277/working/building/REAL300025497970 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497970

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497970/0 /scratch/stefan/7787277/working/building/REAL300025497970 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 853)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/853
`/scratch/stefan/7787277/working/3D/853' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1)

`REAL300025497970.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497970.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497970/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497970 none COC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [187, 187, 179, 179, 179, 108, 108, 108, 108, 108, 77, 37, 77, 13, 1, 1, 1, 1, 1, 1, 1, 108, 187, 201, 201, 201, 187, 187, 187, 187, 179, 108, 108, 108, 108, 108, 37, 37, 1, 108, 108, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [38, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 657
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497970 none COC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [7, 5, 1, 5, 12, 12, 12, 24, 24, 24, 24, 24, 47, 47, 74, 107, 201, 201, 201, 201, 201, 24, 1, 1, 1, 1, 7, 7, 7, 5, 12, 24, 24, 24, 24, 24, 74, 74, 201, 24, 24, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 41, 42, 43, 44, 45, 46, 47, 22, 23, 24, 25] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 499
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497970 none COC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 21, 108, 108, 108, 108, 108, 1, 12, 24, 24, 24, 13, 13, 13, 12, 5, 1, 1, 1, 1, 1, 11, 11, 108, 1, 1, 24, 24, 24, 24, 24, 24, 24] 201
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 40, 21, 39, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 237
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497970 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497970
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497970/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497970
Building REAL300025497971
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497971'
/scratch/stefan/7787277/working/building/REAL300025497971 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497971

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497971/0 /scratch/stefan/7787277/working/building/REAL300025497971 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 854)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/854
`/scratch/stefan/7787277/working/3D/854' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSN=N2)C1)

`REAL300025497971.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497971.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497971/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497971 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSN=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 14, 8, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 22, 49, 141, 141, 141, 141, 141, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 1, 22, 22, 141, 1, 1, 1, 1, 1, 6, 11, 1, 1] 201
rigid atoms, others: [1, 34, 35, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 32, 2, 3, 4, 5, 6, 7, 8, 9, 33, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26])
total number of confs: 272
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497971 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSN=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 14, 8, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 61, 102, 201, 201, 201, 201, 201, 11, 11, 11, 11, 3, 3, 1, 3, 1, 1, 1, 1, 1, 11, 61, 61, 201, 11, 11, 11, 11, 11, 3, 1, 11, 11] 201
rigid atoms, others: [33, 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, 34, 35])
total number of confs: 443
number of broken/clashed sets: 43
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497971 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSN=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 14, 8, 8, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 51, 13, 1, 1, 1, 1, 1, 1, 1, 112, 141, 141, 141, 141, 141, 201, 201, 201, 201, 201, 201, 201, 141, 51, 51, 1, 141, 141, 141, 141, 141, 201, 201, 141, 141] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35])
total number of confs: 635
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497971 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497971
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497971/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497971
Building REAL300025497972
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497972'
/scratch/stefan/7787277/working/building/REAL300025497972 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497972

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497972/0 /scratch/stefan/7787277/working/building/REAL300025497972 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 855)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/855
`/scratch/stefan/7787277/working/3D/855' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1)

`REAL300025497972.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497972.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497972/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497972 none CC(C)C1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [18, 7, 18, 7, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 49, 127, 127, 127, 127, 127, 1, 7, 7, 18, 18, 18, 18, 18, 18, 18, 7, 5, 1, 1, 1, 1, 1, 29, 29, 127, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 310
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497972 none CC(C)C1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 171, 201, 171, 171, 171, 171, 171, 127, 127, 127, 127, 127, 95, 44, 95, 13, 1, 1, 1, 1, 1, 1, 1, 127, 171, 171, 201, 201, 201, 201, 201, 201, 201, 171, 171, 127, 127, 127, 127, 127, 44, 44, 1, 127, 127] 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])
total number of confs: 700
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497972 none CC(C)C1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [4, 1, 4, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 23, 23, 64, 91, 171, 171, 171, 171, 171, 7, 1, 1, 4, 4, 4, 4, 5, 5, 5, 1, 3, 7, 7, 7, 7, 7, 64, 64, 171, 7, 7] 201
rigid atoms, others: [1, 34, 3, 4, 5, 6, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 434
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497972 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497972
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497972/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497972
Building REAL300025497973
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497973'
/scratch/stefan/7787277/working/building/REAL300025497973 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497973

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497973/0 /scratch/stefan/7787277/working/building/REAL300025497973 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 856)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/856
`/scratch/stefan/7787277/working/3D/856' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NOC(C3CC3)=C2)C1)

`REAL300025497973.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497973.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497973/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025497973 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NOC(C3CC3)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 12, 1, 5, 5, 5, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 35, 115, 115, 115, 115, 115, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 24, 24, 5, 1, 19, 19, 115, 1, 1, 1, 1, 1, 5, 24, 24, 24, 24, 24, 5, 1, 1] 201
rigid atoms, others: [32, 1, 34, 43, 33, 10, 11, 12, 13, 14, 15, 26, 42, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 264
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.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: REAL300025497973 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NOC(C3CC3)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 12, 1, 5, 5, 5, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 24, 54, 95, 129, 201, 201, 201, 201, 201, 24, 24, 24, 24, 10, 10, 10, 11, 10, 10, 10, 1, 1, 1, 1, 10, 24, 95, 95, 201, 24, 24, 24, 24, 24, 10, 1, 1, 1, 1, 1, 10, 24, 24] 201
rigid atoms, others: [36, 37, 38, 39, 40, 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, 41, 42, 43])
total number of confs: 542
number of broken/clashed sets: 9
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497973 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NOC(C3CC3)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 12, 1, 5, 5, 5, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 5, 14, 36, 56, 137, 137, 137, 137, 137, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 1, 5, 36, 36, 137, 5, 5, 5, 5, 5, 1, 10, 10, 10, 10, 10, 1, 5, 5] 201
rigid atoms, others: [35, 41, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 42, 43])
total number of confs: 311
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497973 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NOC(C3CC3)=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 12, 1, 5, 5, 5, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 42, 13, 1, 1, 1, 1, 1, 1, 1, 90, 115, 115, 115, 115, 115, 137, 137, 137, 137, 137, 137, 137, 201, 201, 137, 115, 42, 42, 1, 115, 115, 115, 115, 115, 137, 201, 201, 201, 201, 201, 137, 115, 115] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 675
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497973 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497973
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497973/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497973
Building REAL300025497974
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497974'
/scratch/stefan/7787277/working/building/REAL300025497974 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497974

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497974/0 /scratch/stefan/7787277/working/building/REAL300025497974 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 857)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/857
`/scratch/stefan/7787277/working/3D/857' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1)

`REAL300025497974.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497974.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497974/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497974 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens 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, 3, 3, 12, 26, 73, 73, 73, 73, 73, 1, 12, 12, 12, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 12, 12, 73, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12] 201
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 37, 20, 38, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 162
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497974 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 107, 107, 107, 73, 73, 73, 73, 73, 63, 39, 63, 13, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 201, 201, 107, 73, 73, 73, 73, 73, 39, 39, 1, 73, 73, 201, 201, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [36, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 676
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497974 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens need rotated
201  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, 12, 12, 12, 12, 12, 27, 27, 61, 108, 201, 201, 201, 201, 201, 12, 1, 1, 1, 1, 2, 2, 2, 5, 12, 12, 12, 12, 12, 61, 61, 201, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 39, 40, 41, 42, 43, 44, 45, 46, 21, 22, 23, 24] set([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])
total number of confs: 465
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497974 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497974
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497974/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497974
Building REAL300025497975
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497975'
/scratch/stefan/7787277/working/building/REAL300025497975 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497975

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497975/0 /scratch/stefan/7787277/working/building/REAL300025497975 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 858)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/858
`/scratch/stefan/7787277/working/3D/858' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC=C(F)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497975.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497975.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497975/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497975 none CC1=CC=C(F)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens 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, 23, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 31, 83, 83, 83, 83, 83, 1, 23, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 1, 18, 18, 83, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497975 none CC1=CC=C(F)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
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, 107, 107, 107, 83, 83, 83, 83, 83, 67, 36, 67, 13, 1, 1, 1, 1, 1, 1, 1, 83, 201, 201, 201, 201, 201, 201, 107, 83, 83, 83, 83, 83, 36, 36, 1, 83, 83] 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, 42, 43])
total number of confs: 498
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497975 none CC1=CC=C(F)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 1, 15, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 23, 23, 23, 53, 53, 95, 136, 201, 201, 201, 201, 201, 23, 2, 2, 2, 1, 1, 1, 9, 23, 23, 23, 23, 23, 95, 95, 201, 23, 23] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 563
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497975 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497975
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497975/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497975
Building REAL300025497976
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497976'
/scratch/stefan/7787277/working/building/REAL300025497976 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497976

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497976/0 /scratch/stefan/7787277/working/building/REAL300025497976 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 859)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/859
`/scratch/stefan/7787277/working/3D/859' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CO2)C1)

`REAL300025497976.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497976.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497976/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497976 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 46, 136, 136, 136, 136, 136, 1, 1, 1, 1, 1, 1, 6, 6, 6, 9, 9, 9, 9, 1, 21, 21, 136, 1, 1, 1, 1, 1, 6, 9, 9, 1, 1] 201
rigid atoms, others: [1, 35, 36, 10, 11, 12, 13, 14, 15, 23, 27, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 32, 33, 34])
total number of confs: 253
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497976 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 9, 25, 58, 99, 201, 201, 201, 201, 201, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 9, 58, 58, 201, 9, 9, 9, 9, 9, 3, 1, 1, 9, 9] 201
rigid atoms, others: [33, 34, 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, 35, 36])
total number of confs: 443
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497976 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN=CO2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 42, 13, 1, 1, 1, 1, 1, 1, 1, 103, 136, 136, 136, 136, 136, 196, 196, 196, 201, 201, 201, 201, 136, 42, 42, 1, 136, 136, 136, 136, 136, 196, 201, 201, 136, 136] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 26] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36])
total number of confs: 624
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497976 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497976
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497976/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497976
Building REAL300025497977
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497977'
/scratch/stefan/7787277/working/building/REAL300025497977 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497977

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497977/0 /scratch/stefan/7787277/working/building/REAL300025497977 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 860)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/860
`/scratch/stefan/7787277/working/3D/860' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497977.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497977.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497977/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497977 none CC1=NN(C)C(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 29, 67, 67, 67, 67, 67, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 17, 17, 67, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 166
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497977 none CC1=NN(C)C(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
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, 85, 85, 85, 67, 67, 67, 67, 67, 58, 36, 58, 13, 1, 1, 1, 1, 1, 1, 1, 67, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 67, 67, 67, 67, 67, 36, 36, 1, 67, 67] 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])
total number of confs: 454
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497977 none CC1=NN(C)C(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total 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, 18, 18, 18, 18, 18, 47, 47, 86, 132, 201, 201, 201, 201, 201, 18, 2, 2, 2, 2, 2, 2, 2, 2, 2, 6, 18, 18, 18, 18, 18, 86, 86, 201, 18, 18] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 535
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497977 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497977
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497977/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497977
Building REAL300025497978
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497978'
/scratch/stefan/7787277/working/building/REAL300025497978 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497978

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497978/0 /scratch/stefan/7787277/working/building/REAL300025497978 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 861)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/861
`/scratch/stefan/7787277/working/3D/861' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCN1C=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497978.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497978.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497978/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497978 none O=C(CCN1C=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 8, 1, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 20, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 14, 52, 52, 52, 52, 52, 1, 17, 17, 20, 20, 37, 37, 37, 4, 1, 1, 1, 1, 1, 8, 8, 52, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 191
number of broken/clashed sets: 73
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497978 none O=C(CCN1C=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 8, 1, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 74, 74, 117, 124, 201, 201, 201, 201, 52, 52, 52, 52, 52, 37, 25, 37, 12, 1, 1, 1, 1, 1, 1, 1, 52, 117, 117, 124, 124, 201, 201, 201, 74, 52, 52, 52, 52, 52, 25, 25, 1, 52, 52] 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])
total number of confs: 625
number of broken/clashed sets: 73
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497978 none O=C(CCN1C=CN=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 1, 8, 1, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 21, 20, 37, 37, 37, 37, 37, 50, 50, 85, 130, 201, 201, 201, 201, 201, 37, 6, 6, 2, 2, 1, 1, 1, 21, 37, 37, 37, 37, 37, 85, 85, 201, 37, 37] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 553
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497978 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497978
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497978/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497978
Building REAL300025497979
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497979'
/scratch/stefan/7787277/working/building/REAL300025497979 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025497979

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497979/0 /scratch/stefan/7787277/working/building/REAL300025497979 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 862)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/862
`/scratch/stefan/7787277/working/3D/862' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=CN=CN3C=C2)C1)

`REAL300025497979.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497979.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497979/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497979 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=CN=CN3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 5, 7, 7, 6, 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: [5, 1, 5, 14, 23, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 1, 14, 14, 65, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 151
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497979 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=CN=CN3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 5, 7, 7, 6, 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: [37, 15, 37, 73, 105, 201, 201, 201, 201, 201, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 73, 73, 201, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 15, 15] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 511
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497979 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=CN=CN3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 8, 1, 1, 5, 7, 7, 6, 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: [53, 39, 12, 1, 1, 1, 1, 1, 1, 1, 53, 65, 65, 65, 65, 65, 79, 79, 79, 201, 201, 201, 201, 201, 201, 201, 201, 65, 39, 39, 1, 65, 65, 65, 65, 65, 79, 201, 201, 201, 201, 201, 65, 65] 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: 433
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497979 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025497979/1 /scratch/stefan/7787277/working/building/REAL300025497979 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 863)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/863
`/scratch/stefan/7787277/working/3D/863' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=C[NH+]=CN3C=C2)C1)

`REAL300025497979.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025497979.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497979/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497979 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=C[NH+]=CN3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'C.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 1, 8, 1, 1, 5, 7, 7, 6, 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]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 18, 31, 88, 88, 88, 88, 88, 1, 1, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 18, 18, 88, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 14, 1, 1] 166
rigid atoms, others: [32, 1, 34, 35, 36, 33, 44, 10, 11, 12, 13, 14, 15, 43, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 37, 38, 39, 40, 41, 42])
total number of confs: 188
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497979 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=C[NH+]=CN3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'C.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 1, 8, 1, 1, 5, 7, 7, 6, 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]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [36, 14, 36, 63, 98, 166, 166, 166, 166, 166, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 63, 63, 166, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 14, 14] 166
rigid atoms, others: [38, 39, 40, 41, 42, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44])
total number of confs: 415
number of broken/clashed sets: 37
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497979 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC3=C[NH+]=CN3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.cat', 'N.pl3', 'C.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 1, 8, 1, 1, 5, 7, 7, 6, 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]
0  hydrogens need rotated
166  conformations in input
total number of sets (complete confs): 166
using faster count positions algorithm for large data
unique positions, atoms: [72, 50, 13, 1, 1, 1, 1, 1, 1, 1, 72, 88, 88, 88, 88, 88, 106, 106, 106, 166, 166, 166, 166, 166, 166, 166, 166, 166, 88, 50, 50, 1, 88, 88, 88, 88, 88, 106, 166, 166, 166, 166, 166, 88, 88] 166
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])
total number of confs: 437
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497979 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497979
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497979/0.*
1: /scratch/stefan/7787277/working/building/REAL300025497979/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497979
Building REAL300025497980
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497980'
/scratch/stefan/7787277/working/building/REAL300025497980 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497980

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497980/0 /scratch/stefan/7787277/working/building/REAL300025497980 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 864)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/864
`/scratch/stefan/7787277/working/3D/864' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NNC(=O)[N-]C2=O)C1)

`REAL300025497980.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497980.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497980/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497980 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NNC(=O)[N-]C2=O)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7]
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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 4, 15, 36, 103, 103, 103, 103, 103, 1, 1, 1, 1, 1, 1, 4, 4, 4, 21, 21, 21, 21, 21, 21, 21, 1, 15, 15, 103, 1, 1, 1, 1, 1, 4, 21, 1, 1] 201
rigid atoms, others: [32, 1, 34, 37, 38, 33, 10, 11, 12, 13, 14, 15, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36])
total number of confs: 209
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497980 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NNC(=O)[N-]C2=O)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7]
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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [51, 21, 51, 89, 140, 201, 201, 201, 201, 201, 21, 21, 21, 21, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 21, 89, 89, 201, 21, 21, 21, 21, 21, 12, 1, 21, 21] 201
rigid atoms, others: [36, 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, 37, 38])
total number of confs: 543
number of broken/clashed sets: 48
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497980 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NNC(=O)[N-]C2=O)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 8, 1, 11, 8, 1, 11, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 6, 7, 7]
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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [81, 44, 13, 1, 1, 1, 1, 1, 1, 1, 81, 103, 103, 103, 103, 103, 147, 147, 147, 201, 201, 201, 201, 201, 201, 201, 103, 44, 44, 1, 103, 103, 103, 103, 103, 147, 201, 103, 103] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 556
number of broken/clashed sets: 48
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497980 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497980
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497980/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497980
Building REAL300025497981
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497981'
/scratch/stefan/7787277/working/building/REAL300025497981 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497981

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497981/0 /scratch/stefan/7787277/working/building/REAL300025497981 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 865)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/865
`/scratch/stefan/7787277/working/3D/865' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497981.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497981.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497981/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497981 none CC1=NN=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 22, 22, 22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 24, 96, 96, 96, 96, 96, 1, 22, 22, 22, 22, 22, 5, 1, 1, 1, 1, 1, 12, 12, 96, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 185
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497981 none CC1=NN=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 127, 127, 127, 96, 96, 96, 96, 96, 79, 42, 79, 13, 1, 1, 1, 1, 1, 1, 1, 96, 201, 201, 201, 201, 201, 127, 96, 96, 96, 96, 96, 42, 42, 1, 96, 96] 201
rigid atoms, others: [39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41])
total number of confs: 523
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497981 none CC1=NN=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 22, 22, 22, 22, 22, 49, 49, 90, 124, 201, 201, 201, 201, 201, 22, 2, 2, 2, 1, 1, 9, 22, 22, 22, 22, 22, 90, 90, 201, 22, 22] 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])
total number of confs: 556
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497981 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497981
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497981/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497981
Building REAL300025497982
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497982'
/scratch/stefan/7787277/working/building/REAL300025497982 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497982

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497982/0 /scratch/stefan/7787277/working/building/REAL300025497982 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 866)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/866
`/scratch/stefan/7787277/working/3D/866' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CCCC(=O)N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497982.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497982.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497982/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497982 none O=C(CC1CCCC(=O)N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens 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, 23, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 19, 76, 76, 76, 76, 76, 1, 23, 23, 40, 40, 40, 40, 40, 40, 40, 40, 5, 1, 1, 1, 1, 1, 9, 9, 76, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 252
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497982 none O=C(CC1CCCC(=O)N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens 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, 191, 201, 201, 201, 201, 201, 201, 76, 76, 76, 76, 76, 50, 30, 50, 13, 1, 1, 1, 1, 1, 1, 1, 76, 191, 191, 201, 201, 201, 201, 201, 201, 201, 201, 116, 76, 76, 76, 76, 76, 30, 30, 1, 76, 76] 201
rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47])
total number of confs: 768
number of broken/clashed sets: 71
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497982 none O=C(CC1CCCC(=O)N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 40, 40, 40, 40, 40, 54, 54, 87, 129, 201, 201, 201, 201, 201, 40, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 21, 40, 40, 40, 40, 40, 87, 87, 201, 40, 40] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 541
number of broken/clashed sets: 71
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497982 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497982
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497982/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497982
Building REAL300025497983
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497983'
/scratch/stefan/7787277/working/building/REAL300025497983 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497983

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497983/0 /scratch/stefan/7787277/working/building/REAL300025497983 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 867)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/867
`/scratch/stefan/7787277/working/3D/867' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1)

`REAL300025497983.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497983.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497983/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497983 none NC(=O)C1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 12, 13, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 31, 53, 127, 127, 127, 127, 127, 1, 12, 13, 13, 12, 12, 5, 1, 1, 1, 1, 1, 31, 31, 127, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 283
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497983 none NC(=O)C1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 197, 201, 197, 197, 197, 185, 185, 185, 127, 127, 127, 127, 127, 90, 41, 90, 13, 1, 1, 1, 1, 1, 1, 1, 127, 197, 201, 201, 197, 197, 185, 127, 127, 127, 127, 127, 41, 41, 1, 127, 127] 201
rigid atoms, others: [39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41])
total number of confs: 612
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497983 none NC(=O)C1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)O1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 33, 33, 89, 119, 197, 197, 197, 197, 197, 12, 1, 3, 3, 1, 1, 5, 12, 12, 12, 12, 12, 89, 89, 197, 12, 12] 201
rigid atoms, others: [1, 3, 4, 5, 6, 7, 26, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 539
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497983 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497983
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497983/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497983
Building REAL300025497984
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497984'
/scratch/stefan/7787277/working/building/REAL300025497984 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497984

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497984/0 /scratch/stefan/7787277/working/building/REAL300025497984 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 868)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/868
`/scratch/stefan/7787277/working/3D/868' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1Cl)

`REAL300025497984.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497984.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497984/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497984 none CN1N=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 16, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 58, 152, 152, 152, 152, 152, 1, 10, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 1, 32, 32, 152, 1, 1, 10] 201
rigid atoms, others: [32, 33, 34, 38, 6, 7, 8, 9, 10, 11, 12, 22, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40])
total number of confs: 311
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497984 none CN1N=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 16, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 152, 152, 152, 152, 152, 109, 45, 109, 13, 1, 1, 1, 1, 1, 1, 1, 152, 201, 201, 201, 201, 201, 201, 201, 152, 152, 152, 152, 152, 45, 45, 1, 152, 152, 201] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 598
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497984 none CN1N=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1Cl NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.2', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 16, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 10, 10, 10, 10, 10, 31, 31, 85, 124, 201, 201, 201, 201, 201, 10, 1, 1, 1, 2, 2, 2, 3, 10, 10, 10, 10, 10, 85, 85, 201, 10, 10, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 40, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 531
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497984 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497984
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497984/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497984
Building REAL300025497985
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497985'
/scratch/stefan/7787277/working/building/REAL300025497985 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497985

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497985/0 /scratch/stefan/7787277/working/building/REAL300025497985 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 869)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/869
`/scratch/stefan/7787277/working/3D/869' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CN=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1)

`REAL300025497985.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497985.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497985/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497985 none COC1=CN=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 7, 6, 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, 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: [21, 10, 9, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 39, 140, 140, 140, 140, 140, 1, 13, 13, 21, 21, 21, 13, 5, 1, 1, 1, 1, 1, 20, 20, 140, 1, 1, 13] 201
rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 40, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42])
total number of confs: 294
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497985 none COC1=CN=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 140, 140, 140, 140, 140, 106, 44, 106, 13, 1, 1, 1, 1, 1, 1, 1, 140, 201, 201, 201, 201, 201, 201, 201, 140, 140, 140, 140, 140, 44, 44, 1, 140, 140, 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])
total number of confs: 619
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497985 none COC1=CN=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 35, 35, 60, 91, 201, 201, 201, 201, 201, 13, 1, 1, 2, 3, 3, 1, 5, 13, 13, 13, 13, 13, 60, 60, 201, 13, 13, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 42, 25, 26, 30] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 443
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497985 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497985
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497985/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497985
Building REAL300025497986
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497986'
/scratch/stefan/7787277/working/building/REAL300025497986 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497986

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497986/0 /scratch/stefan/7787277/working/building/REAL300025497986 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 870)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/870
`/scratch/stefan/7787277/working/3D/870' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1C)

`REAL300025497986.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497986.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497986/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497986 none COC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 5, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [18, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 30, 53, 168, 168, 168, 168, 168, 1, 8, 8, 8, 18, 18, 18, 8, 5, 1, 1, 1, 1, 1, 30, 30, 168, 1, 1, 8, 8, 8] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44])
total number of confs: 337
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497986 none COC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 5, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 168, 168, 168, 168, 121, 45, 121, 13, 1, 1, 1, 1, 1, 1, 1, 168, 201, 201, 201, 201, 201, 201, 201, 201, 168, 168, 168, 168, 168, 45, 45, 1, 168, 168, 201, 201, 201] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44])
total number of confs: 584
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497986 none COC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 5, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 4, 4, 4, 8, 8, 8, 8, 8, 25, 25, 71, 114, 201, 201, 201, 201, 201, 8, 1, 1, 1, 5, 5, 5, 1, 4, 8, 8, 8, 8, 8, 71, 71, 201, 8, 8, 2, 2, 2] 201
rigid atoms, others: [1, 2, 3, 4, 5, 24, 25, 26, 30] set([0, 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])
total number of confs: 509
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497986 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497986
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497986/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497986
Building REAL300025497987
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497987'
/scratch/stefan/7787277/working/building/REAL300025497987 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497987

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497987/0 /scratch/stefan/7787277/working/building/REAL300025497987 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 871)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/871
`/scratch/stefan/7787277/working/3D/871' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCCC1)

`REAL300025497987.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497987.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497987/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497987 none CC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 14, 45, 45, 45, 45, 45, 1, 26, 26, 26, 26, 26, 26, 26, 26, 11, 11, 5, 1, 1, 1, 1, 1, 8, 8, 45, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 201
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 41, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 165
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497987 none CC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 97, 61, 61, 61, 45, 45, 45, 45, 45, 32, 22, 32, 11, 1, 1, 1, 1, 1, 1, 1, 45, 201, 201, 201, 201, 201, 201, 201, 201, 97, 97, 61, 45, 45, 45, 45, 45, 22, 22, 1, 45, 45, 201, 201, 201, 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, 51, 52])
total number of confs: 717
number of broken/clashed sets: 53
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497987 none CC1(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens need rotated
201  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, 11, 11, 11, 26, 26, 26, 26, 26, 46, 46, 80, 121, 201, 201, 201, 201, 201, 26, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 11, 26, 26, 26, 26, 26, 80, 80, 201, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 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: 545
number of broken/clashed sets: 53
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497987 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497987
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497987/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497987
Building REAL300025497988
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497988'
/scratch/stefan/7787277/working/building/REAL300025497988 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497988

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497988/0 /scratch/stefan/7787277/working/building/REAL300025497988 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 872)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/872
`/scratch/stefan/7787277/working/3D/872' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1)

`REAL300025497988.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497988.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497988/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497988 none CC(C)CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 37, 118, 118, 118, 118, 118, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 18, 18, 118, 1, 1, 9, 9, 9, 9, 9, 9] 201
rigid atoms, others: [37, 38, 7, 8, 9, 10, 11, 12, 13, 46, 45, 40, 41, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44, 47, 48, 49, 50, 51, 52])
total number of confs: 231
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497988 none CC(C)CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations 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, 118, 118, 118, 118, 118, 71, 30, 71, 13, 1, 1, 1, 1, 1, 1, 1, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 144, 118, 118, 118, 118, 118, 30, 30, 1, 118, 118, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [44, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49, 50, 51, 52])
total number of confs: 624
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497988 none CC(C)CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 2, 2, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 34, 34, 73, 113, 201, 201, 201, 201, 201, 9, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 9, 9, 9, 9, 9, 73, 73, 201, 9, 9, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 4, 5, 47, 48, 49, 50, 51, 52, 24, 25, 26] set([0, 1, 2, 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: 491
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497988 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497988
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497988/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497988
Building REAL300025497989
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497989'
/scratch/stefan/7787277/working/building/REAL300025497989 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497989

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497989/0 /scratch/stefan/7787277/working/building/REAL300025497989 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 873)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/873
`/scratch/stefan/7787277/working/3D/873' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCCCCC2)C1)

`REAL300025497989.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497989.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497989/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497989 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCCCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 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]
dock 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: [5, 1, 5, 18, 32, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 1, 5, 5, 5, 22, 22, 22, 22, 22, 22, 22, 1, 18, 18, 79, 1, 1, 1, 1, 1, 5, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 51, 52, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 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])
total number of confs: 216
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497989 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCCCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 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]
dock 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: [53, 22, 53, 96, 136, 201, 201, 201, 201, 201, 22, 22, 22, 22, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 22, 96, 96, 201, 22, 22, 22, 22, 22, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 201
rigid atoms, others: [16, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50] 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, 51, 52])
total number of confs: 558
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497989 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCCCCCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 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]
dock 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: [66, 39, 13, 1, 1, 1, 1, 1, 1, 1, 66, 79, 79, 79, 79, 79, 105, 105, 105, 201, 201, 201, 201, 201, 201, 201, 79, 39, 39, 1, 79, 79, 79, 79, 79, 105, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 79, 79] 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: 640
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497989 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497989
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497989/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497989
Building REAL300025497990
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497990'
/scratch/stefan/7787277/working/building/REAL300025497990 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497990

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497990/0 /scratch/stefan/7787277/working/building/REAL300025497990 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 874)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/874
`/scratch/stefan/7787277/working/3D/874' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC(=O)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025497990.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497990.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497990/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497990 none CN1C=CC(=O)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 1, 1, 1, 11, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [17, 17, 17, 17, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 29, 53, 151, 151, 151, 151, 151, 1, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 29, 29, 151, 1, 1, 17] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 309
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497990 none CN1C=CC(=O)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 1, 1, 1, 11, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 188, 188, 188, 151, 151, 151, 151, 151, 112, 44, 112, 13, 1, 1, 1, 1, 1, 1, 1, 151, 201, 201, 201, 201, 201, 201, 188, 151, 151, 151, 151, 151, 44, 44, 1, 151, 151, 201] 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: 580
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497990 none CN1C=CC(=O)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 8, 1, 1, 1, 11, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 17, 17, 17, 17, 17, 47, 47, 101, 137, 201, 201, 201, 201, 201, 17, 1, 2, 2, 2, 1, 1, 8, 17, 17, 17, 17, 17, 101, 101, 201, 17, 17, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 43, 26, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 568
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497990 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497990
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497990/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497990
Building REAL300025497991
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497991'
/scratch/stefan/7787277/working/building/REAL300025497991 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497991

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497991/0 /scratch/stefan/7787277/working/building/REAL300025497991 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 875)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/875
`/scratch/stefan/7787277/working/3D/875' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3C=CC=CN3C=C2)C1)

`REAL300025497991.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497991.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497991/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497991 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3C=CC=CN3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [6, 1, 6, 20, 35, 112, 112, 112, 112, 112, 1, 1, 1, 1, 1, 1, 5, 5, 5, 20, 20, 20, 20, 20, 20, 20, 20, 1, 20, 20, 112, 1, 1, 1, 1, 1, 5, 20, 20, 20, 20, 20, 20, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 44, 10, 11, 12, 13, 14, 15, 43, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 236
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497991 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3C=CC=CN3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [52, 20, 52, 101, 135, 201, 201, 201, 201, 201, 20, 20, 20, 20, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 101, 101, 201, 20, 20, 20, 20, 20, 8, 1, 1, 1, 1, 1, 1, 20, 20] 201
rigid atoms, others: [37, 38, 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, 43, 44])
total number of confs: 561
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497991 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3C=CC=CN3C=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [89, 43, 13, 1, 1, 1, 1, 1, 1, 1, 89, 112, 112, 112, 112, 112, 153, 153, 153, 201, 201, 201, 201, 201, 201, 201, 201, 112, 43, 43, 1, 112, 112, 112, 112, 112, 153, 201, 201, 201, 201, 201, 201, 112, 112] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 572
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497991 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497991
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497991/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497991
Building REAL300025497992
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497992'
/scratch/stefan/7787277/working/building/REAL300025497992 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497992

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497992/0 /scratch/stefan/7787277/working/building/REAL300025497992 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 876)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/876
`/scratch/stefan/7787277/working/3D/876' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025497992.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497992.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497992/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497992 none COC1=NC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 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]
0  hydrogens 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, 10, 10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 36, 130, 130, 130, 130, 130, 1, 10, 15, 15, 15, 10, 10, 5, 1, 1, 1, 1, 1, 20, 20, 130, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 252
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497992 none COC1=NC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 194, 194, 194, 130, 130, 130, 130, 130, 98, 42, 98, 13, 1, 1, 1, 1, 1, 1, 1, 130, 201, 201, 201, 201, 201, 201, 194, 130, 130, 130, 130, 130, 42, 42, 1, 130, 130] 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])
total number of confs: 612
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497992 none COC1=NC=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 7, 3, 7, 7, 7, 7, 6, 4, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 10, 10, 10, 10, 10, 26, 26, 62, 89, 201, 201, 201, 201, 201, 10, 1, 2, 2, 2, 1, 1, 3, 10, 10, 10, 10, 10, 62, 62, 201, 10, 10] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 442
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497992 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497992
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497992/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497992
Building REAL300025497993
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497993'
/scratch/stefan/7787277/working/building/REAL300025497993 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497993

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497993/0 /scratch/stefan/7787277/working/building/REAL300025497993 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 877)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/877
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2CC3CC2C2CC23)C1)

`REAL300025497993.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497993.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497993/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497993 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3CC2C2CC23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 17, 34, 127, 126, 127, 127, 127, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 1, 18, 18, 127, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 10, 11, 12, 13, 14, 15, 48, 26, 47, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 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])
total number of confs: 244
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497993 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3CC2C2CC23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 13, 35, 71, 106, 201, 201, 201, 201, 201, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 13, 71, 71, 201, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48])
total number of confs: 483
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497993 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3CC2C2CC23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [95, 52, 13, 1, 1, 1, 1, 1, 1, 1, 95, 127, 127, 127, 127, 127, 173, 173, 173, 201, 201, 201, 201, 201, 201, 201, 127, 52, 52, 1, 127, 127, 127, 127, 127, 173, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 127, 127] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 659
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497993 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497993
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497993/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497993
Building REAL300025497994
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497994'
/scratch/stefan/7787277/working/building/REAL300025497994 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497994

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497994/0 /scratch/stefan/7787277/working/building/REAL300025497994 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 878)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/878
`/scratch/stefan/7787277/working/3D/878' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)O1)

`REAL300025497994.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497994.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497994/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497994 none CC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 23, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 32, 87, 87, 87, 87, 87, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 1, 19, 19, 87, 1, 1, 23, 23, 23, 23] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47])
total number of confs: 223
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497994 none CC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 115, 115, 115, 87, 87, 87, 87, 87, 69, 39, 69, 13, 1, 1, 1, 1, 1, 1, 1, 87, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 115, 87, 87, 87, 87, 87, 39, 39, 1, 87, 87, 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])
total number of confs: 657
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497994 none CC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 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, 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, 8, 8, 8, 23, 23, 23, 23, 23, 56, 56, 100, 136, 201, 201, 201, 201, 201, 23, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 8, 23, 23, 23, 23, 23, 100, 100, 201, 23, 23, 1, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 32, 44, 23, 24, 25, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47])
total number of confs: 567
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497994 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497994
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497994/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497994
Building REAL300025497995
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497995'
/scratch/stefan/7787277/working/building/REAL300025497995 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497995

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497995/0 /scratch/stefan/7787277/working/building/REAL300025497995 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 879)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/879
`/scratch/stefan/7787277/working/3D/879' -> `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)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497995.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497995.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497995/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497995 none CC(C)(C)[C@@H]1C[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [42, 26, 42, 42, 26, 26, 26, 4, 26, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 28, 71, 71, 71, 71, 71, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42, 26, 26, 4, 1, 1, 1, 1, 1, 16, 16, 71, 1, 1] 201
rigid atoms, others: [48, 43, 49, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 27, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497995 none CC(C)(C)[C@@H]1C[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 90, 201, 90, 90, 71, 71, 71, 71, 71, 68, 37, 68, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 71, 71, 71, 71, 71, 37, 37, 1, 71, 71] 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])
total number of confs: 626
number of broken/clashed sets: 1
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497995 none CC(C)(C)[C@@H]1C[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 26, 26, 26, 26, 26, 51, 51, 92, 125, 201, 201, 201, 201, 201, 26, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 11, 26, 26, 26, 26, 26, 92, 92, 201, 26, 26] 201
rigid atoms, others: [1, 4, 37, 6, 7, 8, 9, 38, 5] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 551
number of broken/clashed sets: 1
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497995 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497995
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497995/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497995
Building REAL300025497996
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497996'
/scratch/stefan/7787277/working/building/REAL300025497996 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497996

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497996/0 /scratch/stefan/7787277/working/building/REAL300025497996 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 880)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/880
`/scratch/stefan/7787277/working/3D/880' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@]23CCC[C@H]2OCC3)C1)

`REAL300025497996.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497996.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497996/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497996 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@]23CCC[C@H]2OCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 6, 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, 11, 25, 96, 96, 96, 96, 96, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 10, 10, 10, 1, 11, 11, 96, 1, 1, 1, 1, 1, 4, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 47, 10, 11, 12, 13, 14, 15, 48, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 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])
total number of confs: 170
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497996 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@]23CCC[C@H]2OCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 6, 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: [22, 10, 22, 58, 96, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 58, 58, 201, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 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, 47, 48])
total number of confs: 462
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497996 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@]23CCC[C@H]2OCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 7, 12, 5, 5, 5, 7, 7, 6, 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: [75, 42, 13, 1, 1, 1, 1, 1, 1, 1, 75, 96, 96, 96, 96, 96, 131, 131, 131, 201, 201, 201, 201, 201, 201, 201, 201, 96, 42, 42, 1, 96, 96, 96, 96, 96, 131, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 96, 96] 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, 48])
total number of confs: 528
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497996 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497996
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497996/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497996
Building REAL300025497997
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497997'
/scratch/stefan/7787277/working/building/REAL300025497997 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497997

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497997/0 /scratch/stefan/7787277/working/building/REAL300025497997 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 881)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/881
`/scratch/stefan/7787277/working/3D/881' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC1C1CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025497997.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497997.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497997/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025497997 none CC1CC1C1CC1C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [4, 4, 4, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 16, 16, 16, 30, 30, 59, 93, 183, 183, 183, 183, 183, 16, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 6, 16, 16, 16, 16, 16, 59, 59, 183, 16, 16] 201
rigid atoms, others: [33, 34, 3, 4, 5, 6, 7, 35, 36] 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 441
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.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: REAL300025497997 none CC1CC1C1CC1C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 201, 201, 183, 183, 183, 98, 98, 98, 68, 68, 68, 68, 68, 44, 29, 44, 13, 1, 1, 1, 1, 1, 1, 1, 68, 201, 201, 201, 201, 201, 201, 201, 183, 183, 183, 183, 98, 68, 68, 68, 68, 68, 29, 29, 1, 68, 68] 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])
total number of confs: 640
number of broken/clashed sets: 44
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497997 none CC1CC1C1CC1C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [22, 22, 22, 16, 16, 16, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 22, 68, 68, 68, 68, 68, 1, 22, 22, 22, 22, 22, 22, 22, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 12, 12, 68, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 187
number of broken/clashed sets: 44
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497997 none CC1CC1C1CC1C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 22, 22, 22, 22, 22, 40, 40, 73, 111, 201, 201, 201, 201, 201, 22, 2, 2, 2, 1, 1, 1, 1, 4, 4, 4, 4, 11, 22, 22, 22, 22, 22, 73, 73, 201, 22, 22] 201
rigid atoms, others: [0, 1, 2, 3, 4, 32, 29, 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, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 514
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497997 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497997
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497997/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497997
Building REAL300025497998
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497998'
/scratch/stefan/7787277/working/building/REAL300025497998 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497998

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497998/0 /scratch/stefan/7787277/working/building/REAL300025497998 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 882)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/882
`/scratch/stefan/7787277/working/3D/882' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)COC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025497998.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497998.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497998/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497998 none CC1(C)COC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 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, 6, 7, 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: [44, 44, 44, 44, 44, 26, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 24, 66, 66, 66, 66, 66, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 26, 26, 4, 1, 1, 1, 1, 1, 14, 14, 66, 1, 1, 44, 44] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49, 50])
total number of confs: 272
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497998 none CC1(C)COC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 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, 6, 7, 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, 201, 201, 201, 195, 104, 104, 104, 66, 66, 66, 66, 66, 50, 28, 50, 13, 1, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 195, 195, 104, 66, 66, 66, 66, 66, 28, 28, 1, 66, 66, 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, 49, 50])
total number of confs: 758
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497998 none CC1(C)COC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 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, 6, 7, 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: [1, 1, 1, 1, 1, 1, 1, 5, 21, 21, 21, 44, 44, 44, 44, 44, 59, 59, 80, 120, 201, 201, 201, 201, 201, 44, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 5, 5, 21, 44, 44, 44, 44, 44, 80, 80, 201, 44, 44, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 33, 34, 49, 50, 35, 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, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 512
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497998 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497998
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497998/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497998
Building REAL300025497999
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025497999'
/scratch/stefan/7787277/working/building/REAL300025497999 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025497999

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025497999/0 /scratch/stefan/7787277/working/building/REAL300025497999 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 883)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/883
`/scratch/stefan/7787277/working/3D/883' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2OC[C@@H]3CCC[C@@H]32)C1)

`REAL300025497999.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025497999.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025497999/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497999 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2OC[C@@H]3CCC[C@@H]32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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, 1, 1, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 5, 5, 5, 7, 5, 7, 7, 6, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 20, 44, 150, 150, 150, 150, 150, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 21, 21, 150, 1, 1, 1, 1, 1, 4, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 201
rigid atoms, others: [1, 34, 35, 36, 37, 33, 10, 11, 12, 13, 14, 15, 48, 47, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 270
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497999 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2OC[C@@H]3CCC[C@@H]32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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, 1, 1, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 5, 5, 5, 7, 5, 7, 7, 6, 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, 7, 7, 7]
0  hydrogens 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, 18, 48, 92, 201, 201, 201, 201, 201, 7, 7, 7, 7, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 48, 48, 201, 7, 7, 7, 7, 7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 201
rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 48])
total number of confs: 423
number of broken/clashed sets: 33
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025497999 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2OC[C@@H]3CCC[C@@H]32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.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, 1, 1, 5, 8, 1, 11, 5, 7, 12, 5, 5, 7, 5, 5, 5, 5, 7, 5, 7, 7, 6, 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, 7, 7, 7]
0  hydrogens 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, 49, 12, 1, 1, 1, 1, 1, 1, 1, 109, 150, 150, 150, 149, 150, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 49, 49, 1, 150, 150, 150, 150, 149, 201, 201, 201, 201, 201, 201, 201, 201, 201, 149, 149] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 610
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025497999 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025497999
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025497999/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025497999
Building REAL300025498000
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498000'
/scratch/stefan/7787277/working/building/REAL300025498000 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498000

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498000/0 /scratch/stefan/7787277/working/building/REAL300025498000 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 884)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/884
`/scratch/stefan/7787277/working/3D/884' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)C1)

`REAL300025498000.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498000.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498000/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498000 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 20, 42, 124, 124, 124, 124, 124, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 21, 21, 124, 1, 1, 1, 1, 1, 5, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [1, 45, 35, 36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 46, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 40, 41, 42, 43, 44])
total number of confs: 252
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498000 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 61, 99, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 61, 61, 201, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [41, 42, 43, 44, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46])
total number of confs: 459
number of broken/clashed sets: 31
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498000 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@@H]3O[C@H]2[C@H]2C[C@H]23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', '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, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 12, 5, 7, 5, 7, 5, 5, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 37, 12, 1, 1, 1, 1, 1, 1, 1, 88, 123, 124, 123, 124, 124, 177, 177, 177, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 37, 37, 1, 124, 124, 124, 124, 124, 177, 201, 201, 201, 201, 124, 123] 201
rigid atoms, others: [34, 3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 661
number of broken/clashed sets: 31
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498000 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498000
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498000/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498000
Building REAL300025498001
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498001'
/scratch/stefan/7787277/working/building/REAL300025498001 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498001

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498001/0 /scratch/stefan/7787277/working/building/REAL300025498001 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 885)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/885
`/scratch/stefan/7787277/working/3D/885' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O)

`REAL300025498001.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498001.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498001/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498001 none CN1C=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 49, 143, 143, 143, 143, 143, 1, 20, 20, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 28, 28, 143, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 301
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498001 none CN1C=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 182, 182, 182, 143, 143, 143, 143, 143, 104, 39, 104, 13, 1, 1, 1, 1, 1, 1, 1, 143, 201, 201, 201, 201, 201, 201, 201, 201, 182, 143, 143, 143, 143, 143, 39, 39, 1, 143, 143] 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])
total number of confs: 575
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498001 none CN1C=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 6, 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, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 49, 49, 103, 133, 201, 201, 201, 201, 201, 20, 1, 1, 2, 2, 2, 1, 1, 1, 9, 20, 20, 20, 20, 20, 103, 103, 201, 20, 20] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 25, 26, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 571
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498001 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498001
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498001/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498001
Building REAL300025498002
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498002'
/scratch/stefan/7787277/working/building/REAL300025498002 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498002

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498002/0 /scratch/stefan/7787277/working/building/REAL300025498002 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 886)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/886
`/scratch/stefan/7787277/working/3D/886' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=NO1)

`REAL300025498002.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498002.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498002/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498002 none CCC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 20, 37, 104, 104, 104, 104, 104, 1, 5, 5, 14, 14, 14, 14, 14, 5, 5, 1, 1, 1, 1, 1, 20, 20, 104, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 251
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498002 none CCC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 121, 121, 121, 121, 121, 121, 104, 104, 104, 104, 104, 79, 39, 79, 13, 1, 1, 1, 1, 1, 1, 1, 104, 121, 121, 201, 201, 201, 201, 201, 121, 121, 104, 104, 104, 104, 104, 39, 39, 1, 104, 104] 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])
total number of confs: 856
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498002 none CCC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 12, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [4, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 14, 14, 37, 58, 121, 121, 121, 121, 121, 5, 1, 1, 4, 5, 5, 4, 4, 1, 1, 5, 5, 5, 5, 5, 37, 37, 121, 5, 5] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 297
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498002 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498002
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498002/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498002
Building REAL300025498003
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498003'
/scratch/stefan/7787277/working/building/REAL300025498003 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498003

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498003/0 /scratch/stefan/7787277/working/building/REAL300025498003 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 887)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/887
`/scratch/stefan/7787277/working/3D/887' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C)

`REAL300025498003.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498003.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498003/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498003 none CCC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 11, 8, 5, 1, 1, 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, 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]
0  hydrogens need 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, 179, 76, 76, 76, 51, 51, 51, 51, 51, 44, 26, 44, 12, 1, 1, 1, 1, 1, 1, 1, 51, 192, 201, 200, 201, 201, 201, 201, 201, 192, 179, 179, 76, 51, 51, 51, 51, 51, 26, 26, 1, 51, 51, 201, 201, 201, 201, 200, 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])
total number of confs: 877
number of broken/clashed sets: 109
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498003 none CCC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 11, 8, 5, 1, 1, 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, 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]
0  hydrogens 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, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 13, 51, 51, 51, 51, 51, 1, 33, 38, 37, 37, 37, 37, 37, 36, 33, 23, 23, 5, 1, 1, 1, 1, 1, 6, 6, 51, 1, 1, 38, 38, 38, 38, 37, 38, 38] 201
rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 44, 43, 22, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 271
number of broken/clashed sets: 109
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498003 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498003
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498003/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498003
Building REAL300025498004
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498004'
/scratch/stefan/7787277/working/building/REAL300025498004 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498004

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498004/0 /scratch/stefan/7787277/working/building/REAL300025498004 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 888)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/888
`/scratch/stefan/7787277/working/3D/888' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[NH+](C)CCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498004.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498004.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498004/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498004 none C[NH+](C)CCCCC(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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, 10, 12, 10, 10, 10, 9, 9, 9, 9, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 1, 1, 9, 12, 12, 12, 12, 12, 12, 12, 12, 11, 12, 12, 12, 12, 12, 10, 9, 9, 9, 9, 9, 9, 9, 1, 9, 9] 12
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: 53
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: REAL300025498004 none C[NH+](C)CCCCC(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [8, 6, 8, 8, 5, 3, 5, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 5, 9, 9, 9, 9, 9, 1, 8, 8, 8, 8, 8, 8, 6, 6, 4, 5, 5, 5, 5, 5, 3, 1, 1, 1, 1, 1, 4, 4, 9, 1, 1] 12
rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 16, 50, 51, 46, 26, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49])
total number of confs: 70
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498004 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498004
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498004/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498004
Building REAL300025498005
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498005'
/scratch/stefan/7787277/working/building/REAL300025498005 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498005

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498005/0 /scratch/stefan/7787277/working/building/REAL300025498005 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 889)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/889
`/scratch/stefan/7787277/working/3D/889' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=C1)

`REAL300025498005.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498005.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498005/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498005 none C#CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.ar', 'C.ar', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 10, 10, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 35, 60, 159, 159, 159, 159, 159, 1, 10, 10, 10, 10, 10, 6, 1, 1, 1, 1, 1, 35, 35, 159, 1, 1, 10] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41])
total number of confs: 324
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498005 none C#CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.ar', 'C.ar', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 159, 159, 159, 159, 159, 118, 45, 118, 13, 1, 1, 1, 1, 1, 1, 1, 158, 201, 201, 201, 201, 201, 201, 159, 159, 159, 159, 159, 45, 45, 1, 159, 159, 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])
total number of confs: 607
number of broken/clashed sets: 32
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498005 none C#CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.ar', 'C.ar', '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, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 30, 30, 84, 121, 201, 201, 201, 201, 201, 10, 1, 1, 1, 1, 1, 4, 10, 10, 10, 10, 10, 84, 84, 201, 10, 10, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 25, 26, 27, 28, 29] set([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])
total number of confs: 503
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498005 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498005
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498005/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498005
Building REAL300025498006
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498006'
/scratch/stefan/7787277/working/building/REAL300025498006 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498006

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498006/0 /scratch/stefan/7787277/working/building/REAL300025498006 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 890)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/890
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2=CC=CC=C2)C1)

`REAL300025498006.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498006.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498006/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025498006 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 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: [6, 1, 6, 17, 28, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 1, 4, 4, 4, 30, 30, 30, 30, 30, 44, 44, 44, 44, 44, 1, 17, 17, 73, 1, 1, 1, 1, 1, 4, 30, 30, 44, 44, 44, 44, 44, 1, 1] 201
rigid atoms, others: [1, 34, 35, 36, 37, 33, 10, 11, 12, 13, 14, 15, 46, 47, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 236
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.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: REAL300025498006 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 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: [78, 44, 78, 124, 154, 201, 201, 201, 201, 201, 44, 44, 44, 44, 20, 20, 4, 20, 4, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 44, 124, 124, 201, 44, 44, 44, 44, 44, 20, 4, 4, 1, 1, 1, 1, 1, 44, 44] 201
rigid atoms, others: [41, 42, 43, 44, 45, 21, 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, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47])
total number of confs: 595
number of broken/clashed sets: 2
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498006 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 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: [63, 30, 63, 112, 146, 201, 201, 201, 201, 201, 30, 30, 30, 30, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 4, 4, 3, 4, 4, 30, 112, 112, 201, 30, 30, 30, 30, 30, 11, 1, 1, 4, 4, 3, 4, 4, 30, 30] 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])
total number of confs: 592
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498006 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@H]2C2=CC=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 1, 1, 1, 1, 1, 5, 7, 7, 6, 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: [66, 35, 13, 1, 1, 1, 1, 1, 1, 1, 66, 73, 73, 73, 73, 73, 103, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 73, 35, 35, 1, 73, 73, 73, 73, 73, 103, 201, 201, 201, 201, 201, 201, 201, 73, 73] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 645
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498006 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498006
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498006/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498006
Building REAL300025498007
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498007'
/scratch/stefan/7787277/working/building/REAL300025498007 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498007

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498007/0 /scratch/stefan/7787277/working/building/REAL300025498007 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 891)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/891
`/scratch/stefan/7787277/working/3D/891' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2CCC(=O)N2)C1)

`REAL300025498007.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498007.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498007/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498007 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 18, 37, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 1, 5, 5, 5, 16, 16, 16, 16, 16, 16, 1, 18, 18, 126, 1, 1, 1, 1, 1, 5, 16, 16, 16, 16, 16, 1, 1] 201
rigid atoms, others: [32, 1, 33, 40, 41, 10, 11, 12, 13, 14, 15, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39])
total number of confs: 254
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498007 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 16, 37, 75, 104, 201, 201, 201, 201, 201, 16, 16, 16, 16, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 16, 75, 75, 201, 16, 16, 16, 16, 16, 9, 1, 1, 1, 1, 1, 16, 16] 201
rigid atoms, others: [35, 36, 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, 40, 41])
total number of confs: 498
number of broken/clashed sets: 24
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498007 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [92, 44, 12, 1, 1, 1, 1, 1, 1, 1, 92, 126, 126, 126, 126, 126, 186, 186, 186, 201, 201, 201, 201, 201, 201, 126, 44, 44, 1, 126, 126, 126, 126, 126, 186, 201, 201, 201, 201, 201, 126, 126] 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: 626
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498007 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498007
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498007/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498007
Building REAL300025498008
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498008'
/scratch/stefan/7787277/working/building/REAL300025498008 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498008

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498008/0 /scratch/stefan/7787277/working/building/REAL300025498008 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 892)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/892
`/scratch/stefan/7787277/working/3D/892' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498008.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498008.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498008/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498008 none CC(=O)N1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens 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, 19, 14, 14, 14, 14, 5, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 43, 110, 110, 110, 110, 110, 1, 19, 19, 19, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 24, 24, 110, 1, 1] 201
rigid atoms, others: [47, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 268
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498008 none CC(=O)N1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 186, 201, 186, 186, 186, 186, 160, 186, 160, 160, 110, 110, 110, 110, 110, 82, 28, 82, 12, 1, 1, 1, 1, 1, 1, 1, 110, 201, 201, 201, 186, 186, 186, 186, 186, 186, 160, 110, 110, 110, 110, 110, 28, 28, 1, 110, 110] 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, 46, 47])
total number of confs: 603
number of broken/clashed sets: 35
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498008 none CC(=O)N1CCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 14, 14, 14, 14, 14, 34, 34, 80, 114, 186, 186, 186, 186, 186, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 8, 14, 14, 14, 14, 14, 80, 80, 186, 14, 14] 201
rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 35, 36, 33, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 484
number of broken/clashed sets: 35
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498008 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498008
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498008/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498008
Building REAL300025498009
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498009'
/scratch/stefan/7787277/working/building/REAL300025498009 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498009

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498009/0 /scratch/stefan/7787277/working/building/REAL300025498009 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 893)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/893
`/scratch/stefan/7787277/working/3D/893' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N[C@@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C)

`REAL300025498009.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498009.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498009/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498009 none CC(=O)N[C@@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 187, 118, 187, 118, 118, 78, 78, 78, 78, 78, 58, 34, 58, 13, 1, 1, 1, 1, 1, 1, 1, 78, 187, 201, 191, 201, 201, 201, 201, 118, 78, 78, 78, 78, 78, 34, 34, 1, 78, 78, 201, 201, 201, 201, 201, 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, 46, 47, 48, 49])
total number of confs: 902
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: REAL300025498009 none CC(=O)N[C@@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)C NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 11, 8, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7]
0  hydrogens 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, 20, 5, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 78, 78, 78, 78, 78, 1, 20, 28, 24, 28, 28, 28, 28, 5, 1, 1, 1, 1, 1, 9, 9, 78, 1, 1, 28, 28, 28, 28, 28, 28, 28] 201
rigid atoms, others: [33, 34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 14, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 278
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498009 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498009
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498009/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498009
Building REAL300025498010
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498010'
/scratch/stefan/7787277/working/building/REAL300025498010 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498010

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498010/0 /scratch/stefan/7787277/working/building/REAL300025498010 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 894)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/894
`/scratch/stefan/7787277/working/3D/894' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CC=C1)

`REAL300025498010.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498010.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498010/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498010 none C[C@@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 124, 201, 124, 124, 89, 89, 89, 89, 89, 78, 37, 78, 13, 1, 1, 1, 1, 1, 1, 1, 89, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 89, 89, 89, 89, 89, 37, 37, 1, 89, 89, 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])
total number of confs: 801
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498010 none C[C@@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 10, 10, 10, 28, 28, 28, 28, 28, 58, 58, 104, 137, 201, 201, 201, 201, 201, 28, 1, 1, 1, 1, 1, 1, 3, 3, 3, 10, 28, 28, 28, 28, 28, 104, 104, 201, 28, 28, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 42, 43, 44, 45, 46, 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])
total number of confs: 556
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498010 none C[C@@H](C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CC=CC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 1, 1, 1, 1, 7, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 6, 22, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 33, 89, 89, 89, 89, 89, 1, 22, 28, 28, 22, 28, 28, 22, 22, 22, 6, 1, 1, 1, 1, 1, 20, 20, 89, 1, 1, 28, 28, 22, 28, 28] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 41] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46])
total number of confs: 271
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498010 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498010
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498010/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498010
Building REAL300025498011
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498011'
/scratch/stefan/7787277/working/building/REAL300025498011 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498011

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498011/0 /scratch/stefan/7787277/working/building/REAL300025498011 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 895)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/895
`/scratch/stefan/7787277/working/3D/895' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1CC[C@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1)

`REAL300025498011.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498011.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498011/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498011 none C[C@H]1CC[C@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 4, 19, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 32, 73, 73, 73, 73, 73, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 1, 1, 1, 1, 1, 18, 18, 73, 1, 1, 19, 19, 19, 19] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49])
total number of confs: 195
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498011 none C[C@H]1CC[C@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 95, 201, 95, 95, 73, 73, 73, 73, 73, 63, 34, 63, 13, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 201, 201, 201, 201, 95, 73, 73, 73, 73, 73, 34, 34, 1, 73, 73, 201, 201, 201, 201] 201
rigid atoms, others: [43, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49])
total number of confs: 634
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498011 none C[C@H]1CC[C@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 19, 19, 19, 19, 19, 47, 47, 100, 143, 201, 201, 201, 201, 201, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 19, 19, 19, 19, 19, 100, 100, 201, 19, 19, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 46, 47, 48, 49, 26, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 563
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498011 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498011
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498011/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498011
Building REAL300025498012
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498012'
/scratch/stefan/7787277/working/building/REAL300025498012 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498012

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498012/0 /scratch/stefan/7787277/working/building/REAL300025498012 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 896)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/896
`/scratch/stefan/7787277/working/3D/896' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@H]1CC[C@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1)

`REAL300025498012.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498012.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498012/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498012 none CC[C@H]1CC[C@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens 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, 20, 20, 20, 20, 20, 5, 20, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 28, 74, 74, 74, 74, 74, 1, 20, 20, 26, 28, 28, 28, 28, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 17, 17, 74, 1, 1, 20, 20, 20, 20] 201
rigid atoms, others: [48, 43, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49, 50, 51, 52])
total number of confs: 249
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498012 none CC[C@H]1CC[C@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens 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, 201, 201, 201, 83, 201, 83, 83, 74, 74, 74, 74, 74, 65, 37, 65, 13, 1, 1, 1, 1, 1, 1, 1, 74, 201, 201, 197, 201, 201, 201, 201, 201, 201, 201, 201, 83, 74, 74, 74, 74, 74, 37, 37, 1, 74, 74, 201, 201, 201, 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, 48, 49, 50, 51, 52])
total number of confs: 613
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498012 none CC[C@H]1CC[C@H](C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 20, 20, 20, 20, 20, 49, 49, 76, 116, 201, 201, 201, 201, 201, 20, 1, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 6, 20, 20, 20, 20, 20, 76, 76, 201, 20, 20, 1, 1, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 51, 34, 49, 50, 35, 52, 36, 27, 28, 37] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 487
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498012 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498012
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498012/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498012
Building REAL300025498013
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498013'
/scratch/stefan/7787277/working/building/REAL300025498013 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498013

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498013/0 /scratch/stefan/7787277/working/building/REAL300025498013 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 897)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/897
`/scratch/stefan/7787277/working/3D/897' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=CC=C2Cl)C1)

`REAL300025498013.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498013.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498013/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498013 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=CC=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 16, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 35, 99, 99, 99, 99, 99, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 1, 18, 18, 99, 1, 1, 1, 1, 1, 4, 11, 11, 11, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37])
total number of confs: 205
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498013 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=CC=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 16, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 33, 66, 106, 201, 201, 201, 201, 201, 11, 11, 11, 11, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 11, 66, 66, 201, 11, 11, 11, 11, 11, 5, 1, 1, 1, 11, 11] 201
rigid atoms, others: [35, 36, 37, 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, 38, 39])
total number of confs: 463
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498013 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=CC=C2Cl)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 16, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [71, 35, 13, 1, 1, 1, 1, 1, 1, 1, 71, 99, 99, 99, 99, 99, 141, 141, 141, 201, 201, 201, 201, 201, 201, 99, 35, 35, 1, 99, 99, 99, 99, 99, 141, 201, 201, 201, 99, 99] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 558
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498013 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498013
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498013/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498013
Building REAL300025498014
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498014'
/scratch/stefan/7787277/working/building/REAL300025498014 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498014

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498014/0 /scratch/stefan/7787277/working/building/REAL300025498014 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 898)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/898
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2=CC=C(Cl)C=N2)C1)

`REAL300025498014.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498014.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498014/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498014 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(Cl)C=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 8, 5, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 20, 45, 132, 132, 132, 132, 132, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 8, 1, 20, 20, 132, 1, 1, 1, 1, 1, 5, 8, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37])
total number of confs: 248
number of broken/clashed sets: 29
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498014 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(Cl)C=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 8, 5, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 8, 25, 57, 97, 201, 201, 201, 201, 201, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 8, 57, 57, 201, 8, 8, 8, 8, 8, 3, 1, 1, 1, 8, 8] 201
rigid atoms, others: [35, 36, 37, 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, 38, 39])
total number of confs: 435
number of broken/clashed sets: 29
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498014 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(Cl)C=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 16, 1, 8, 5, 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, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [98, 40, 13, 1, 1, 1, 1, 1, 1, 1, 98, 132, 132, 132, 132, 132, 201, 201, 201, 201, 201, 201, 201, 201, 201, 132, 40, 40, 1, 132, 132, 132, 132, 132, 201, 201, 201, 201, 132, 132] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 28] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 633
number of broken/clashed sets: 29
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498014 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498014
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498014/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498014
Building REAL300025498015
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498015'
/scratch/stefan/7787277/working/building/REAL300025498015 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498015

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498015/0 /scratch/stefan/7787277/working/building/REAL300025498015 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 899)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/899
`/scratch/stefan/7787277/working/3D/899' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(F)=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498015.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498015.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498015/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498015 none CC1=CC(F)=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens 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, 5, 5, 23, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 30, 70, 70, 70, 70, 70, 1, 23, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 1, 17, 17, 70, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 209
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498015 none CC1=CC(F)=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  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, 201, 201, 92, 92, 92, 70, 70, 70, 70, 70, 58, 36, 58, 13, 1, 1, 1, 1, 1, 1, 1, 70, 201, 201, 201, 201, 201, 201, 92, 70, 70, 70, 70, 70, 36, 36, 1, 70, 70] 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, 42, 43])
total number of confs: 708
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498015 none CC1=CC(F)=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 1, 15, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 23, 23, 23, 52, 52, 89, 131, 201, 201, 201, 201, 201, 23, 2, 2, 2, 1, 1, 1, 9, 23, 23, 23, 23, 23, 89, 89, 201, 23, 23] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 544
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498015 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498015
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498015/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498015
Building REAL300025498016
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498016'
/scratch/stefan/7787277/working/building/REAL300025498016 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498016

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498016/0 /scratch/stefan/7787277/working/building/REAL300025498016 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 900)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/900
`/scratch/stefan/7787277/working/3D/900' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[NH+](C)C)

`REAL300025498016.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498016.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498016/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498016 none CC(C)C(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 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
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [56, 69, 69, 55, 55, 55, 29, 29, 29, 29, 29, 29, 23, 29, 12, 1, 1, 1, 1, 1, 1, 1, 29, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 55, 29, 29, 29, 29, 29, 23, 23, 1, 29, 29, 69, 69, 69, 69, 69, 69] 69
rigid atoms, others: [43, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 348
number of broken/clashed sets: 68
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498016 none CC(C)C(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)[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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 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
69  conformations in input
total number of sets (complete confs): 69
using faster count positions algorithm for large data
unique positions, atoms: [8, 11, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 10, 29, 29, 29, 29, 29, 1, 11, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12, 11, 5, 1, 1, 1, 1, 1, 8, 8, 29, 1, 1, 13, 13, 13, 13, 13, 13] 69
rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 12, 45, 44, 40, 22, 39, 38] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46, 47, 48, 49, 50, 51])
total number of confs: 146
number of broken/clashed sets: 68
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498016 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498016
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498016/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498016
Building REAL300025498017
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498017'
/scratch/stefan/7787277/working/building/REAL300025498017 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025498017

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498017/0 /scratch/stefan/7787277/working/building/REAL300025498017 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 901)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/901
`/scratch/stefan/7787277/working/3D/901' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC[N@H+](C)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498017.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498017.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498017/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498017 none CCC[N@H+](C)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
128  conformations in input
total number of sets (complete confs): 128
using faster count positions algorithm for large data
unique positions, atoms: [128, 128, 128, 128, 128, 128, 128, 114, 114, 114, 104, 104, 104, 104, 104, 96, 34, 95, 13, 1, 1, 1, 1, 1, 1, 1, 104, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 128, 114, 104, 104, 104, 104, 104, 34, 34, 1, 104, 104] 128
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: 425
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: REAL300025498017 none CCC[N@H+](C)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [14, 14, 9, 8, 9, 9, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 26, 104, 104, 104, 104, 104, 1, 14, 14, 14, 14, 14, 14, 14, 9, 9, 9, 8, 8, 7, 7, 3, 1, 1, 1, 1, 1, 12, 12, 104, 1, 1] 128
rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 16, 50, 51, 46, 26, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49])
total number of confs: 224
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498017 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025498017/1 /scratch/stefan/7787277/working/building/REAL300025498017 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 902)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/902
`/scratch/stefan/7787277/working/3D/902' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC[N@@H+](C)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498017.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025498017.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498017/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498017 none CCC[N@@H+](C)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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, 13, 13, 13, 9, 9, 9, 9, 9, 9, 8, 9, 7, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 9, 9, 9, 9, 9, 8, 8, 1, 9, 9] 19
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: 70
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: REAL300025498017 none CCC[N@@H+](C)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 5, 9, 6, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
19  conformations in input
total number of sets (complete confs): 19
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 9, 9, 9, 9, 9, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 4, 4, 9, 1, 1] 19
rigid atoms, others: [45, 43, 44, 42, 11, 12, 13, 14, 15, 16, 50, 51, 46, 26, 10] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49])
total number of confs: 53
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498017 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498017
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498017/0.*
1: /scratch/stefan/7787277/working/building/REAL300025498017/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498017
Building REAL300025498018
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498018'
/scratch/stefan/7787277/working/building/REAL300025498018 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498018

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498018/0 /scratch/stefan/7787277/working/building/REAL300025498018 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 903)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/903
`/scratch/stefan/7787277/working/3D/903' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CNC(=O)C1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1)

`REAL300025498018.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498018.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498018/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498018 none CNC(=O)C1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 7, 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: [25, 25, 20, 25, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 34, 71, 71, 71, 71, 71, 1, 20, 20, 20, 25, 25, 25, 25, 5, 1, 1, 1, 1, 1, 20, 20, 71, 1, 1, 20, 20, 20, 20, 20, 20] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47])
total number of confs: 219
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498018 none CNC(=O)C1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 7, 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, 201, 201, 114, 114, 114, 71, 71, 71, 71, 71, 57, 36, 57, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 201, 201, 114, 71, 71, 71, 71, 71, 36, 36, 1, 71, 71, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 622
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498018 none CNC(=O)C1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 7, 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, 20, 20, 20, 20, 20, 54, 54, 98, 138, 201, 201, 201, 201, 201, 20, 1, 1, 1, 5, 5, 5, 5, 6, 20, 20, 20, 20, 20, 98, 98, 201, 20, 20, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 4, 5, 42, 43, 44, 45, 46, 47, 24, 25, 26] set([0, 1, 3, 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])
total number of confs: 549
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498018 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498018
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498018/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498018
Building REAL300025498019
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498019'
/scratch/stefan/7787277/working/building/REAL300025498019 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498019

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498019/0 /scratch/stefan/7787277/working/building/REAL300025498019 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 904)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/904
`/scratch/stefan/7787277/working/3D/904' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=C1)

`REAL300025498019.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498019.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498019/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498019 none COC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 34, 98, 98, 98, 98, 98, 1, 17, 17, 17, 22, 22, 22, 5, 1, 1, 1, 1, 1, 20, 20, 98, 1, 1, 17, 17] 201
rigid atoms, others: [32, 33, 34, 38, 6, 7, 8, 9, 10, 11, 12, 22, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41])
total number of confs: 225
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498019 none COC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 131, 131, 131, 98, 98, 98, 98, 98, 75, 38, 75, 13, 1, 1, 1, 1, 1, 1, 1, 98, 201, 201, 201, 201, 201, 201, 131, 98, 98, 98, 98, 98, 38, 38, 1, 98, 98, 201, 201] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41])
total number of confs: 520
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498019 none COC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)SC=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 14, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 5, 5, 5, 17, 17, 17, 17, 17, 42, 42, 84, 116, 201, 201, 201, 201, 201, 17, 1, 1, 1, 4, 4, 4, 5, 17, 17, 17, 17, 17, 84, 84, 201, 17, 17, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 40, 41, 23, 24, 25] set([0, 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])
total number of confs: 518
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498019 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498019
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498019/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498019
Building REAL300025498020
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498020'
/scratch/stefan/7787277/working/building/REAL300025498020 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025498020

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498020/0 /scratch/stefan/7787277/working/building/REAL300025498020 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 905)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/905
`/scratch/stefan/7787277/working/3D/905' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC[N@H+](C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498020.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498020.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498020/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498020 none CCC[N@H+](C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 9, 6, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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, 59, 61, 61, 42, 42, 42, 25, 25, 25, 25, 25, 25, 21, 25, 13, 1, 1, 1, 1, 1, 1, 1, 25, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 59, 59, 42, 25, 25, 25, 25, 25, 21, 21, 1, 25, 25] 61
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: 244
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: REAL300025498020 none CCC[N@H+](C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 9, 6, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
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: [14, 14, 12, 9, 12, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 25, 25, 25, 25, 25, 1, 14, 14, 14, 14, 14, 14, 14, 12, 12, 12, 9, 9, 4, 1, 1, 1, 1, 1, 5, 5, 25, 1, 1] 61
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 108
number of broken/clashed sets: 46
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498020 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025498020/1 /scratch/stefan/7787277/working/building/REAL300025498020 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 906)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/906
`/scratch/stefan/7787277/working/3D/906' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC[N@@H+](C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498020.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025498020.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498020/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498020 none CCC[N@@H+](C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 9, 6, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [22, 22, 22, 20, 22, 22, 16, 16, 16, 10, 10, 10, 10, 10, 10, 8, 10, 7, 1, 1, 1, 1, 1, 1, 1, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 20, 20, 16, 10, 10, 10, 10, 10, 8, 8, 1, 10, 10] 22
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: 80
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: REAL300025498020 none CCC[N@@H+](C)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 9, 6, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
22  conformations in input
total number of sets (complete confs): 22
using default count positions algorithm for smaller data
unique positions, atoms: [9, 9, 8, 6, 8, 8, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 10, 10, 10, 10, 10, 1, 9, 9, 9, 9, 9, 9, 9, 8, 8, 8, 6, 6, 4, 1, 1, 1, 1, 1, 5, 5, 10, 1, 1] 22
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 62
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498020 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498020
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498020/0.*
1: /scratch/stefan/7787277/working/building/REAL300025498020/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498020
Building REAL300025498021
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498021'
/scratch/stefan/7787277/working/building/REAL300025498021 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498021

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498021/0 /scratch/stefan/7787277/working/building/REAL300025498021 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 907)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/907
`/scratch/stefan/7787277/working/3D/907' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(C)(C)C)

`REAL300025498021.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498021.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498021/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498021 none CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 11, 8, 5, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 124, 124, 124, 98, 98, 98, 98, 98, 59, 30, 59, 13, 1, 1, 1, 1, 1, 1, 1, 98, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 124, 98, 98, 98, 98, 98, 30, 30, 1, 98, 98, 201, 201, 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, 51])
total number of confs: 780
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: REAL300025498021 none CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 11, 8, 5, 1, 1, 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, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 24, 98, 98, 98, 98, 98, 1, 26, 26, 26, 26, 26, 26, 26, 26, 21, 21, 5, 1, 1, 1, 1, 1, 13, 13, 98, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26] 201
rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 21, 41, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51])
total number of confs: 257
number of broken/clashed sets: 105
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498021 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498021
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498021/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498021
Building REAL300025498022
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498022'
/scratch/stefan/7787277/working/building/REAL300025498022 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498022

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498022/0 /scratch/stefan/7787277/working/building/REAL300025498022 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 908)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/908
`/scratch/stefan/7787277/working/3D/908' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498022.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498022.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498022/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498022 none COC1=CC=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 12, 12, 12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 33, 134, 134, 134, 134, 134, 1, 19, 19, 19, 12, 12, 12, 5, 1, 1, 1, 1, 1, 18, 18, 134, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 257
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498022 none COC1=CC=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 180, 180, 180, 134, 134, 134, 134, 134, 105, 44, 105, 13, 1, 1, 1, 1, 1, 1, 1, 134, 201, 201, 201, 201, 201, 201, 180, 134, 134, 134, 134, 134, 44, 44, 1, 134, 134] 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, 42, 43])
total number of confs: 613
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498022 none COC1=CC=CN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 1, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 34, 34, 68, 98, 201, 201, 201, 201, 201, 12, 3, 3, 3, 1, 1, 1, 4, 12, 12, 12, 12, 12, 68, 68, 201, 12, 12] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 470
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498022 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498022
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498022/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498022
Building REAL300025498023
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498023'
/scratch/stefan/7787277/working/building/REAL300025498023 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498023

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498023/0 /scratch/stefan/7787277/working/building/REAL300025498023 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 909)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/909
`/scratch/stefan/7787277/working/3D/909' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCCCOCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498023.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498023.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498023/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498023 none CCCCCCOCC(=O)NC1C=CCN(C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 116, 91, 73, 28, 28, 28, 25, 25, 25, 25, 25, 24, 21, 24, 11, 1, 1, 1, 1, 1, 1, 1, 25, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 116, 116, 73, 73, 28, 25, 25, 25, 25, 25, 21, 21, 1, 25, 25] 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: 865
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: REAL300025498023 none CCCCCCOCC(=O)NC1C=CCN(C(=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', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [45, 45, 45, 45, 22, 13, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 9, 25, 25, 25, 25, 25, 1, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 22, 22, 7, 7, 3, 1, 1, 1, 1, 1, 7, 7, 25, 1, 1] 201
rigid atoms, others: [11, 47, 44, 10, 43, 12, 13, 14, 45, 16, 51, 52, 46, 26, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 48, 49, 50])
total number of confs: 236
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498023 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498023
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498023/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498023
Building REAL300025498024
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498024'
/scratch/stefan/7787277/working/building/REAL300025498024 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498024

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498024/0 /scratch/stefan/7787277/working/building/REAL300025498024 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 910)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/910
`/scratch/stefan/7787277/working/3D/910' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3NC=CN3N=C2)C1)

`REAL300025498024.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498024.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498024/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498024 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3NC=CN3N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 8, 1, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 1, 16, 16, 101, 1, 1, 1, 1, 1, 5, 17, 17, 17, 17, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 41, 10, 11, 12, 13, 14, 15, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38, 39])
total number of confs: 202
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498024 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3NC=CN3N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 8, 1, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 17, 36, 76, 108, 201, 201, 201, 201, 201, 17, 17, 17, 17, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 17, 76, 76, 201, 17, 17, 17, 17, 17, 7, 1, 1, 1, 1, 17, 17] 201
rigid atoms, others: [36, 37, 38, 39, 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, 40, 41])
total number of confs: 503
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498024 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3NC=CN3N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 8, 1, 5, 7, 7, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 41, 13, 1, 1, 1, 1, 1, 1, 1, 73, 103, 103, 103, 103, 103, 145, 145, 145, 201, 201, 201, 201, 201, 201, 201, 103, 41, 41, 1, 103, 103, 103, 103, 103, 145, 201, 201, 201, 201, 103, 103] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 559
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498024 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498024
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498024/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498024
Building REAL300025498025
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498025'
/scratch/stefan/7787277/working/building/REAL300025498025 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498025

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498025/0 /scratch/stefan/7787277/working/building/REAL300025498025 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 911)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/911
`/scratch/stefan/7787277/working/3D/911' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCO1)

`REAL300025498025.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498025.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498025/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498025 none CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 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, 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]
0  hydrogens need 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, 105, 105, 105, 72, 72, 72, 72, 72, 53, 29, 53, 13, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 201, 201, 201, 201, 201, 199, 199, 105, 72, 72, 72, 72, 72, 29, 29, 1, 72, 72, 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])
total number of confs: 779
number of broken/clashed sets: 77
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498025 none CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 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, 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]
0  hydrogens 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, 20, 20, 20, 31, 31, 31, 31, 31, 40, 40, 82, 124, 201, 201, 201, 201, 201, 31, 1, 1, 1, 1, 1, 4, 4, 4, 4, 9, 9, 20, 31, 31, 31, 31, 31, 82, 82, 201, 31, 31, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 44, 45, 46, 47, 48, 49, 50, 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: 553
number of broken/clashed sets: 77
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498025 none CC(CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 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, 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]
0  hydrogens 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, 16, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 15, 72, 72, 72, 72, 72, 1, 28, 31, 31, 31, 31, 28, 28, 28, 28, 16, 16, 4, 1, 1, 1, 1, 1, 8, 8, 72, 1, 1, 31, 31, 31, 31, 31, 31, 31] 201
rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 43, 21, 38, 42, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 240
number of broken/clashed sets: 77
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498025 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498025
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498025/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498025
Building REAL300025498026
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498026'
/scratch/stefan/7787277/working/building/REAL300025498026 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498026

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498026/0 /scratch/stefan/7787277/working/building/REAL300025498026 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 912)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/912
`/scratch/stefan/7787277/working/3D/912' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COCCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1)

`REAL300025498026.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498026.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498026/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498026 none COCCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 7, 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: [47, 29, 19, 12, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 24, 52, 52, 52, 52, 52, 1, 12, 12, 12, 47, 47, 47, 29, 29, 19, 19, 4, 1, 1, 1, 1, 1, 14, 14, 52, 1, 1, 12, 12, 12, 12, 12, 12] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46, 47, 48, 49, 50])
total number of confs: 263
number of broken/clashed sets: 36
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498026 none COCCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 7, 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, 179, 153, 101, 101, 101, 52, 52, 52, 52, 52, 42, 22, 42, 13, 1, 1, 1, 1, 1, 1, 1, 52, 153, 153, 153, 201, 201, 201, 201, 201, 179, 179, 101, 52, 52, 52, 52, 52, 22, 22, 1, 52, 52, 153, 153, 153, 153, 153, 153] 201
rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 752
number of broken/clashed sets: 36
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498026 none COCCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 7, 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: [24, 11, 6, 1, 1, 1, 5, 5, 5, 12, 12, 12, 12, 12, 17, 17, 39, 66, 153, 153, 153, 153, 153, 12, 1, 1, 1, 24, 24, 24, 11, 11, 6, 6, 5, 12, 12, 12, 12, 12, 39, 39, 153, 12, 12, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [3, 4, 5, 45, 46, 47, 48, 49, 50, 24, 25, 26] set([0, 1, 2, 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: 384
number of broken/clashed sets: 36
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498026 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498026
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498026/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498026
Building REAL300025498027
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498027'
/scratch/stefan/7787277/working/building/REAL300025498027 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498027

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498027/0 /scratch/stefan/7787277/working/building/REAL300025498027 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 913)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/913
`/scratch/stefan/7787277/working/3D/913' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC[C@@H](NC(N)=O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498027.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498027.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498027/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498027 none CCC[C@@H](NC(N)=O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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, 7]
0  hydrogens need rotated
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, 81, 162, 162, 179, 179, 179, 81, 81, 52, 52, 52, 52, 52, 42, 30, 42, 12, 1, 1, 1, 1, 1, 1, 1, 52, 201, 201, 201, 201, 201, 201, 201, 179, 179, 179, 81, 52, 52, 52, 52, 52, 30, 30, 1, 52, 52] 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, 48])
total number of confs: 941
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: REAL300025498027 none CCC[C@@H](NC(N)=O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [30, 28, 16, 5, 16, 16, 21, 21, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 11, 52, 52, 52, 52, 52, 1, 30, 30, 30, 30, 30, 30, 30, 21, 21, 21, 5, 1, 1, 1, 1, 1, 8, 8, 52, 1, 1] 201
rigid atoms, others: [48, 43, 47, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 230
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498027 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498027
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498027/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498027
Building REAL300025498028
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498028'
/scratch/stefan/7787277/working/building/REAL300025498028 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498028

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498028/0 /scratch/stefan/7787277/working/building/REAL300025498028 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 914)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/914
`/scratch/stefan/7787277/working/3D/914' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC1=CC=CC=C1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498028.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498028.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498028/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498028 none C#CC1=CC=CC=C1CC(=O)NC1C=CCN(C(=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.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 37, 25, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 14, 53, 53, 53, 53, 53, 1, 37, 37, 37, 37, 37, 25, 25, 5, 1, 1, 1, 1, 1, 8, 8, 53, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 44, 11, 12, 13, 14, 15, 16, 17, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 190
number of broken/clashed sets: 37
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498028 none C#CC1=CC=CC=C1CC(=O)NC1C=CCN(C(=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.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 184, 75, 75, 75, 53, 53, 53, 53, 53, 41, 27, 41, 12, 1, 1, 1, 1, 1, 1, 1, 53, 201, 201, 201, 201, 201, 184, 184, 75, 53, 53, 53, 53, 53, 27, 27, 1, 53, 53] 201
rigid atoms, others: [43, 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, 44, 45])
total number of confs: 734
number of broken/clashed sets: 37
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498028 none C#CC1=CC=CC=C1CC(=O)NC1C=CCN(C(=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.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 22, 22, 22, 37, 37, 37, 37, 37, 49, 49, 82, 118, 201, 201, 201, 201, 201, 37, 1, 1, 1, 1, 1, 5, 5, 22, 37, 37, 37, 37, 37, 82, 82, 201, 37, 37] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 536
number of broken/clashed sets: 37
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498028 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498028
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498028/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498028
Building REAL300025498029
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498029'
/scratch/stefan/7787277/working/building/REAL300025498029 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498029

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498029/0 /scratch/stefan/7787277/working/building/REAL300025498029 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 915)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/915
`/scratch/stefan/7787277/working/3D/915' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)NC=N1)

`REAL300025498029.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498029.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498029/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498029 none CC1=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [43, 43, 30, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 14, 62, 62, 62, 62, 62, 1, 43, 43, 43, 43, 43, 43, 30, 30, 5, 1, 1, 1, 1, 1, 10, 9, 62, 1, 1, 43, 43] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43])
total number of confs: 221
number of broken/clashed sets: 73
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498029 none CC1=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 197, 99, 99, 99, 62, 62, 62, 62, 62, 41, 30, 41, 13, 1, 1, 1, 1, 1, 1, 1, 62, 201, 201, 201, 201, 201, 201, 197, 197, 99, 62, 62, 62, 62, 62, 30, 30, 1, 62, 62, 201, 201] 201
rigid atoms, others: [39, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43])
total number of confs: 741
number of broken/clashed sets: 73
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498029 none CC1=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.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, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 6, 22, 22, 22, 43, 43, 43, 43, 43, 56, 56, 88, 126, 201, 201, 201, 201, 201, 43, 1, 1, 1, 2, 2, 2, 6, 6, 22, 43, 43, 43, 43, 43, 88, 88, 201, 43, 43, 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: 555
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498029 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498029
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498029/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498029
Building REAL300025498030
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498030'
/scratch/stefan/7787277/working/building/REAL300025498030 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498030

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498030/0 /scratch/stefan/7787277/working/building/REAL300025498030 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 916)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/916
`/scratch/stefan/7787277/working/3D/916' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1C(=O)[N-]NC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498030.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498030.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498030/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498030 none O=C(CN1C(=O)[N-]NC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 8, 8, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 6, 6, 27, 52, 150, 150, 150, 150, 150, 1, 12, 12, 12, 5, 1, 1, 1, 1, 1, 27, 27, 150, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 40, 10, 11, 12, 13, 14, 15, 16, 26, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 306
number of broken/clashed sets: 48
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498030 none O=C(CN1C(=O)[N-]NC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 8, 8, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 201, 201, 201, 201, 201, 201, 201, 150, 150, 150, 150, 150, 123, 33, 123, 13, 1, 1, 1, 1, 1, 1, 1, 150, 201, 201, 201, 189, 150, 150, 150, 150, 150, 33, 33, 1, 150, 150] 201
rigid atoms, others: [38, 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, 39, 40])
total number of confs: 612
number of broken/clashed sets: 48
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498030 none O=C(CN1C(=O)[N-]NC1=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 8, 1, 11, 8, 8, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 17, 17, 46, 46, 100, 134, 201, 201, 201, 201, 201, 17, 2, 2, 1, 6, 17, 17, 17, 17, 17, 100, 100, 201, 17, 17] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 546
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498030 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498030
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498030/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498030
Building REAL300025498031
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498031'
/scratch/stefan/7787277/working/building/REAL300025498031 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498031

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498031/0 /scratch/stefan/7787277/working/building/REAL300025498031 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 917)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/917
`/scratch/stefan/7787277/working/3D/917' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C)

`REAL300025498031.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498031.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498031/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498031 none COC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 36, 112, 112, 112, 112, 112, 1, 13, 13, 13, 13, 17, 17, 17, 5, 1, 1, 1, 1, 1, 20, 20, 112, 1, 1, 13, 13, 13, 13] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44])
total number of confs: 236
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498031 none COC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 165, 165, 165, 112, 112, 112, 112, 112, 83, 42, 83, 13, 1, 1, 1, 1, 1, 1, 1, 112, 201, 201, 201, 201, 201, 201, 201, 165, 112, 112, 112, 112, 112, 42, 42, 1, 112, 112, 201, 201, 201, 201] 201
rigid atoms, others: [38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44])
total number of confs: 595
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498031 none COC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=NN1C NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need 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, 4, 4, 4, 13, 13, 13, 13, 13, 39, 39, 84, 128, 201, 201, 201, 201, 201, 13, 1, 1, 1, 1, 3, 3, 3, 4, 13, 13, 13, 13, 13, 84, 84, 201, 13, 13, 1, 2, 2, 2] 201
rigid atoms, others: [1, 2, 3, 4, 41, 23, 24, 25, 26] set([0, 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, 42, 43, 44])
total number of confs: 538
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498031 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498031
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498031/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498031
Building REAL300025498032
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498032'
/scratch/stefan/7787277/working/building/REAL300025498032 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498032

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498032/0 /scratch/stefan/7787277/working/building/REAL300025498032 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 918)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/918
`/scratch/stefan/7787277/working/3D/918' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(F)(F)C(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498032.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498032.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498032/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498032 none CC(F)(F)C(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 15, 15, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 12, 12, 9, 12, 12, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 6, 1, 1, 1, 1, 1, 1, 1, 8, 12, 12, 12, 12, 12, 12, 12, 12, 12, 9, 8, 8, 8, 8, 8, 8, 8, 1, 8, 8] 12
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])
total number of confs: 41
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: REAL300025498032 none CC(F)(F)C(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 15, 15, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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
12  conformations in input
total number of sets (complete confs): 12
using default count positions algorithm for smaller data
unique positions, atoms: [7, 7, 7, 7, 5, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 7, 7, 8, 8, 8, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 7, 7, 8, 1, 1] 12
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 47
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498032 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498032
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498032/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498032
Building REAL300025498033
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498033'
/scratch/stefan/7787277/working/building/REAL300025498033 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025498033

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498033/0 /scratch/stefan/7787277/working/building/REAL300025498033 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 919)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/919
`/scratch/stefan/7787277/working/3D/919' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CC[N@H+](C2)CCC3)C1)

`REAL300025498033.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498033.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498033/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498033 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CC[N@H+](C2)CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 6, 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, 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
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [3, 1, 3, 7, 11, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 7, 7, 20, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 20
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 49, 50, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 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: 54
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498033 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CC[N@H+](C2)CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 6, 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, 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
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [6, 4, 6, 12, 15, 20, 20, 20, 20, 20, 4, 4, 4, 4, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 12, 12, 20, 4, 4, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 20
rigid atoms, others: [16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 49, 50])
total number of confs: 64
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498033 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CC[N@H+](C2)CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 6, 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, 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
20  conformations in input
total number of sets (complete confs): 20
using default count positions algorithm for smaller data
unique positions, atoms: [19, 17, 11, 1, 1, 1, 1, 1, 1, 1, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 17, 17, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 20
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 55
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498033 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025498033/1 /scratch/stefan/7787277/working/building/REAL300025498033 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 920)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/920
`/scratch/stefan/7787277/working/3D/920' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CC[N@@H+](C2)CCC3)C1)

`REAL300025498033.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025498033.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498033/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498033 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CC[N@@H+](C2)CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 6, 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, 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
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 10, 16, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 1, 10, 10, 40, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 51
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 49, 50, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 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: 98
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498033 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CC[N@@H+](C2)CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 6, 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, 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
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [14, 6, 14, 21, 30, 51, 51, 51, 51, 51, 6, 6, 6, 6, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 21, 21, 51, 6, 6, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 51
rigid atoms, others: [16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 49, 50])
total number of confs: 133
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498033 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C23CC[N@@H+](C2)CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 9, 6, 5, 5, 5, 5, 5, 7, 7, 6, 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, 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
51  conformations in input
total number of sets (complete confs): 51
using faster count positions algorithm for large data
unique positions, atoms: [37, 32, 13, 1, 1, 1, 1, 1, 1, 1, 37, 40, 40, 40, 40, 40, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 40, 32, 32, 1, 40, 40, 40, 40, 40, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 40, 40] 51
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 171
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498033 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498033
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498033/0.*
1: /scratch/stefan/7787277/working/building/REAL300025498033/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498033
Building REAL300025498034
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498034'
/scratch/stefan/7787277/working/building/REAL300025498034 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498034

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498034/0 /scratch/stefan/7787277/working/building/REAL300025498034 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 921)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/921
`/scratch/stefan/7787277/working/3D/921' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(=O)N(C)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498034.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498034.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498034/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498034 none CC(=O)N(C)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 198, 201, 183, 146, 64, 64, 64, 56, 56, 56, 56, 56, 46, 28, 46, 13, 1, 1, 1, 1, 1, 1, 1, 56, 201, 201, 201, 201, 201, 201, 198, 198, 191, 191, 146, 146, 64, 56, 56, 56, 56, 56, 28, 28, 1, 56, 56] 201
rigid atoms, others: [47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49])
total number of confs: 938
number of broken/clashed sets: 139
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498034 none CC(=O)N(C)CCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 32, 38, 20, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 18, 56, 56, 56, 56, 56, 1, 38, 38, 38, 38, 38, 38, 32, 32, 24, 24, 14, 14, 4, 1, 1, 1, 1, 1, 9, 9, 56, 1, 1] 201
rigid atoms, others: [48, 43, 40, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 285
number of broken/clashed sets: 139
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498034 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498034
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498034/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498034
Building REAL300025498035
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498035'
/scratch/stefan/7787277/working/building/REAL300025498035 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498035

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498035/0 /scratch/stefan/7787277/working/building/REAL300025498035 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 922)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/922
`/scratch/stefan/7787277/working/3D/922' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NOC(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025498035.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498035.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498035/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498035 none CC1=NOC(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 17, 14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 14, 61, 61, 61, 61, 61, 1, 27, 27, 27, 27, 17, 17, 14, 14, 5, 1, 1, 1, 1, 1, 7, 7, 61, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 173
number of broken/clashed sets: 75
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498035 none CC1=NOC(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 165, 163, 94, 94, 94, 61, 61, 61, 61, 61, 52, 30, 52, 13, 1, 1, 1, 1, 1, 1, 1, 61, 201, 201, 201, 201, 165, 165, 163, 163, 94, 61, 61, 61, 61, 61, 30, 30, 1, 61, 61] 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])
total number of confs: 714
number of broken/clashed sets: 75
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498035 none CC1=NOC(CCC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 6, 9, 20, 21, 21, 27, 27, 27, 27, 27, 37, 37, 74, 122, 201, 201, 201, 201, 201, 27, 1, 2, 2, 2, 6, 6, 9, 9, 21, 27, 27, 27, 27, 27, 74, 74, 201, 27, 27] 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: 527
number of broken/clashed sets: 75
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498035 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498035
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498035/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498035
Building REAL300025498036
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498036'
/scratch/stefan/7787277/working/building/REAL300025498036 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498036

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498036/0 /scratch/stefan/7787277/working/building/REAL300025498036 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 923)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/923
`/scratch/stefan/7787277/working/3D/923' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498036.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498036.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498036/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498036 none CC1=NNC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 4, 4, 15, 46, 143, 143, 143, 143, 143, 1, 13, 13, 13, 12, 13, 6, 1, 1, 1, 1, 1, 15, 15, 143, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 253
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498036 none CC1=NNC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 143, 143, 143, 143, 143, 123, 50, 123, 13, 1, 1, 1, 1, 1, 1, 1, 143, 201, 201, 201, 201, 201, 195, 143, 143, 143, 143, 143, 50, 50, 1, 143, 143] 201
rigid atoms, others: [38, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40])
total number of confs: 613
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498036 none CC1=NNC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 63, 114, 201, 201, 201, 201, 201, 13, 2, 2, 2, 1, 1, 6, 13, 13, 13, 13, 13, 63, 63, 201, 13, 13] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 479
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498036 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498036
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498036/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498036
Building REAL300025498037
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498037'
/scratch/stefan/7787277/working/building/REAL300025498037 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498037

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498037/0 /scratch/stefan/7787277/working/building/REAL300025498037 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 924)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/924
`/scratch/stefan/7787277/working/3D/924' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025498037.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498037.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498037/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498037 none CCCC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens 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, 19, 7, 7, 7, 7, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 33, 88, 88, 88, 88, 88, 1, 7, 21, 21, 21, 21, 21, 19, 19, 7, 5, 1, 1, 1, 1, 1, 19, 19, 88, 1, 1, 7] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46])
total number of confs: 256
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498037 none CCCC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
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, 115, 111, 111, 111, 88, 88, 88, 88, 88, 70, 38, 70, 13, 1, 1, 1, 1, 1, 1, 1, 88, 115, 201, 201, 201, 201, 201, 201, 201, 115, 111, 88, 88, 88, 88, 88, 38, 38, 1, 88, 88, 115] 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: 884
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498037 none CCCC1=NNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 6, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 17, 17, 37, 57, 115, 115, 115, 115, 115, 7, 1, 8, 8, 8, 8, 8, 6, 6, 1, 4, 7, 7, 7, 7, 7, 37, 37, 115, 7, 7, 1] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 34, 46, 26] set([0, 1, 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, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 300
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498037 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498037
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498037/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498037
Building REAL300025498038
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498038'
/scratch/stefan/7787277/working/building/REAL300025498038 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498038

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498038/0 /scratch/stefan/7787277/working/building/REAL300025498038 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 925)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/925
`/scratch/stefan/7787277/working/3D/925' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC3=NNC=C32)C1)

`REAL300025498038.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498038.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498038/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498038 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC3=NNC=C32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 5, 7, 7, 6, 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, 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, 12, 19, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 1, 12, 12, 70, 1, 1, 1, 1, 1, 5, 24, 24, 24, 24, 24, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 154
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498038 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC3=NNC=C32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 5, 7, 7, 6, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [52, 24, 52, 92, 120, 201, 201, 201, 201, 201, 24, 24, 24, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 92, 92, 201, 24, 24, 24, 24, 24, 9, 1, 1, 1, 1, 1, 24, 24] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 547
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498038 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC3=NNC=C32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'C.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 8, 1, 1, 5, 7, 7, 6, 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, 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: [53, 35, 13, 1, 1, 1, 1, 1, 1, 1, 53, 70, 70, 70, 70, 70, 107, 107, 107, 201, 201, 201, 201, 201, 201, 201, 201, 70, 35, 35, 1, 70, 70, 70, 70, 70, 107, 201, 201, 201, 201, 201, 70, 70] 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: 496
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498038 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498038
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498038/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498038
Building REAL300025498039
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498039'
/scratch/stefan/7787277/working/building/REAL300025498039 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498039

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498039/0 /scratch/stefan/7787277/working/building/REAL300025498039 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 926)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/926
`/scratch/stefan/7787277/working/3D/926' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC3=CNN=C32)C1)

`REAL300025498039.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498039.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498039/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498039 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC3=CNN=C32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 20, 45, 139, 139, 139, 139, 139, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 1, 20, 20, 139, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 254
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498039 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC3=CNN=C32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 10, 32, 67, 111, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 67, 67, 201, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 461
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498039 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CC3=CNN=C32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.pl3', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 43, 13, 1, 1, 1, 1, 1, 1, 1, 105, 139, 139, 139, 139, 139, 199, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 139, 43, 43, 1, 139, 139, 139, 139, 139, 199, 201, 201, 201, 201, 201, 139, 139] 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: 621
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498039 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498039
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498039/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498039
Building REAL300025498040
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498040'
/scratch/stefan/7787277/working/building/REAL300025498040 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498040

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498040/0 /scratch/stefan/7787277/working/building/REAL300025498040 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 927)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/927
`/scratch/stefan/7787277/working/3D/927' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1)

`REAL300025498040.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498040.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498040/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498040 none C#CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 49, 157, 157, 157, 157, 157, 1, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 22, 22, 157, 1, 1, 8, 8] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42])
total number of confs: 299
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498040 none C#CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 157, 157, 157, 157, 157, 124, 54, 124, 13, 1, 1, 1, 1, 1, 1, 1, 157, 201, 201, 201, 201, 201, 201, 157, 157, 157, 157, 157, 54, 54, 1, 157, 157, 201, 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: 607
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498040 none C#CC1=CC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 8, 8, 8, 8, 8, 34, 34, 73, 125, 201, 201, 201, 201, 201, 8, 1, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 73, 73, 201, 8, 8, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 25, 26, 27, 28, 29] set([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])
total number of confs: 483
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498040 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498040
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498040/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498040
Building REAL300025498041
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498041'
/scratch/stefan/7787277/working/building/REAL300025498041 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025498041

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498041/0 /scratch/stefan/7787277/working/building/REAL300025498041 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 928)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/928
`/scratch/stefan/7787277/working/3D/928' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)NN=N1)

`REAL300025498041.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498041.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498041/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498041 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)NN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.pl3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [17, 17, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 26, 72, 72, 72, 72, 72, 1, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 12, 12, 72, 1, 1, 17] 201
rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 37, 21, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39])
total number of confs: 156
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498041 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)NN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.pl3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 93, 93, 93, 72, 72, 72, 72, 72, 57, 36, 57, 13, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 201, 201, 93, 72, 72, 72, 72, 72, 36, 36, 1, 72, 72, 201] 201
rigid atoms, others: [36, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39])
total number of confs: 459
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498041 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)NN=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.pl3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 17, 17, 33, 33, 64, 96, 201, 201, 201, 201, 201, 17, 1, 1, 1, 2, 2, 2, 7, 17, 17, 17, 17, 17, 64, 64, 201, 17, 17, 1] 201
rigid atoms, others: [0, 1, 2, 3, 39, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 488
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498041 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025498041/1 /scratch/stefan/7787277/working/building/REAL300025498041 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 929)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/929
`/scratch/stefan/7787277/working/3D/929' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498041.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025498041.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498041/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498041 none CC1=NNN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 17, 52, 147, 147, 147, 147, 147, 1, 9, 9, 9, 9, 6, 1, 1, 1, 1, 1, 18, 17, 147, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 39, 8, 9, 10, 11, 12, 13, 14, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 262
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498041 none CC1=NNN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 147, 147, 147, 147, 147, 124, 54, 124, 13, 1, 1, 1, 1, 1, 1, 1, 147, 201, 201, 201, 201, 201, 147, 147, 147, 147, 147, 54, 54, 1, 147, 147] 201
rigid atoms, others: [37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 626
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498041 none CC1=NNN=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 9, 9, 9, 9, 9, 21, 21, 53, 110, 201, 201, 201, 201, 201, 9, 2, 2, 2, 1, 4, 9, 9, 9, 9, 9, 53, 53, 201, 9, 9] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 439
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498041 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498041
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498041/0.*
1: /scratch/stefan/7787277/working/building/REAL300025498041/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498041
Building REAL300025498042
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498042'
/scratch/stefan/7787277/working/building/REAL300025498042 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498042

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498042/0 /scratch/stefan/7787277/working/building/REAL300025498042 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 930)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/930
`/scratch/stefan/7787277/working/3D/930' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CC=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025498042.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498042.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498042/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498042 none COC1=CC=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 38, 137, 137, 137, 137, 137, 1, 8, 13, 13, 13, 8, 8, 5, 1, 1, 1, 1, 1, 21, 21, 137, 1, 1, 8] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 264
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498042 none COC1=CC=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 200, 200, 200, 137, 137, 137, 137, 137, 104, 42, 104, 13, 1, 1, 1, 1, 1, 1, 1, 137, 201, 201, 201, 201, 201, 201, 200, 137, 137, 137, 137, 137, 42, 42, 1, 137, 137, 201] 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: 612
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498042 none COC1=CC=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [7, 3, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 8, 8, 8, 8, 8, 27, 27, 65, 96, 201, 201, 201, 201, 201, 8, 1, 3, 3, 3, 1, 1, 4, 8, 8, 8, 8, 8, 65, 65, 201, 8, 8, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 43, 26, 30, 31] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 461
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498042 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498042
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498042/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498042
Building REAL300025498043
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498043'
/scratch/stefan/7787277/working/building/REAL300025498043 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498043

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498043/0 /scratch/stefan/7787277/working/building/REAL300025498043 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 931)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/931
`/scratch/stefan/7787277/working/3D/931' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=CSC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025498043.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498043.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498043/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498043 none COC1=CSC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 14, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 18, 18, 18, 18, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 21, 40, 110, 110, 110, 110, 110, 1, 18, 28, 28, 28, 18, 4, 1, 1, 1, 1, 1, 21, 21, 110, 1, 1, 18] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41])
total number of confs: 250
number of broken/clashed sets: 6
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498043 none COC1=CSC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 14, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 159, 159, 159, 110, 110, 110, 110, 110, 88, 39, 88, 13, 1, 1, 1, 1, 1, 1, 1, 110, 201, 201, 201, 201, 201, 159, 110, 110, 110, 110, 110, 39, 39, 1, 110, 110, 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])
total number of confs: 593
number of broken/clashed sets: 6
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498043 none COC1=CSC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 12, 1, 1, 14, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 36, 36, 80, 110, 201, 201, 201, 201, 201, 18, 1, 3, 3, 3, 1, 6, 18, 18, 18, 18, 18, 80, 80, 201, 18, 18, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 41, 25, 29] set([0, 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])
total number of confs: 490
number of broken/clashed sets: 6
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498043 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498043
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498043/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498043
Building REAL300025498044
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498044'
/scratch/stefan/7787277/working/building/REAL300025498044 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498044

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498044/0 /scratch/stefan/7787277/working/building/REAL300025498044 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 932)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/932
`/scratch/stefan/7787277/working/3D/932' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)CCC1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498044.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498044.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498044/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498044 none CN1C(=O)CCC1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [25, 25, 25, 25, 25, 25, 19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 14, 26, 96, 96, 96, 96, 96, 1, 25, 25, 25, 25, 25, 25, 25, 25, 19, 19, 5, 1, 1, 1, 1, 1, 14, 14, 96, 1, 1] 201
rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 245
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498044 none CN1C(=O)CCC1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 198, 120, 120, 120, 96, 96, 96, 96, 96, 57, 31, 57, 13, 1, 1, 1, 1, 1, 1, 1, 96, 201, 201, 201, 201, 201, 201, 201, 201, 198, 198, 120, 96, 96, 96, 96, 96, 31, 31, 1, 96, 96] 201
rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47])
total number of confs: 746
number of broken/clashed sets: 45
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498044 none CN1C(=O)CCC1CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 4, 13, 13, 13, 25, 25, 25, 25, 25, 54, 54, 90, 127, 201, 201, 201, 201, 201, 25, 2, 2, 2, 1, 1, 1, 1, 1, 4, 4, 13, 25, 25, 25, 25, 25, 90, 90, 201, 25, 25] 201
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])
total number of confs: 563
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498044 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498044
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498044/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498044
Building REAL300025498045
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498045'
/scratch/stefan/7787277/working/building/REAL300025498045 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498045

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498045/0 /scratch/stefan/7787277/working/building/REAL300025498045 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 933)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/933
`/scratch/stefan/7787277/working/3D/933' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=CC=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498045.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498045.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498045/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498045 none O=C(CCC1=CC=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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: [5, 5, 5, 19, 23, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 18, 78, 78, 78, 78, 78, 1, 19, 19, 23, 23, 31, 31, 31, 31, 5, 1, 1, 1, 1, 1, 10, 10, 78, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 44, 10, 11, 12, 13, 14, 15, 16, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 227
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498045 none O=C(CCC1=CC=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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: [116, 116, 116, 187, 201, 201, 201, 201, 201, 201, 78, 78, 78, 78, 78, 56, 30, 56, 13, 1, 1, 1, 1, 1, 1, 1, 78, 187, 187, 201, 201, 201, 201, 201, 201, 116, 78, 78, 78, 78, 78, 30, 30, 1, 78, 78] 201
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, 44, 45])
total number of confs: 755
number of broken/clashed sets: 66
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498045 none O=C(CCC1=CC=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 1, 1, 1, 1, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 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: [19, 10, 6, 1, 1, 1, 1, 1, 1, 1, 19, 19, 31, 31, 31, 31, 31, 41, 41, 75, 119, 201, 201, 201, 201, 201, 31, 10, 10, 6, 6, 1, 1, 1, 1, 19, 31, 31, 31, 31, 31, 75, 75, 201, 31, 31] 201
rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 534
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498045 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498045
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498045/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498045
Building REAL300025498046
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498046'
/scratch/stefan/7787277/working/building/REAL300025498046 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498046

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498046/0 /scratch/stefan/7787277/working/building/REAL300025498046 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 934)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/934
`/scratch/stefan/7787277/working/3D/934' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC1=NN(C)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498046.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498046.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498046/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498046 none COC1=NN(C)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 3, 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: [13, 13, 13, 13, 13, 13, 13, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 45, 150, 150, 150, 150, 150, 1, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 26, 26, 150, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 44, 10, 11, 12, 13, 14, 15, 16, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 291
number of broken/clashed sets: 22
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498046 none COC1=NN(C)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 3, 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, 201, 201, 197, 197, 197, 150, 150, 150, 150, 150, 109, 46, 109, 13, 1, 1, 1, 1, 1, 1, 1, 150, 201, 201, 201, 201, 201, 201, 201, 197, 150, 150, 150, 150, 150, 46, 46, 1, 150, 150] 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, 43, 44])
total number of confs: 599
number of broken/clashed sets: 22
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498046 none COC1=NN(C)C=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 12, 1, 8, 8, 5, 1, 1, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [7, 3, 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, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 38, 38, 89, 122, 201, 201, 201, 201, 201, 13, 2, 2, 2, 2, 2, 2, 1, 4, 13, 13, 13, 13, 13, 89, 89, 201, 13, 13] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 33] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 544
number of broken/clashed sets: 22
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498046 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498046
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498046/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498046
Building REAL300025498047
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498047'
/scratch/stefan/7787277/working/building/REAL300025498047 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498047

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498047/0 /scratch/stefan/7787277/working/building/REAL300025498047 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 935)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/935
`/scratch/stefan/7787277/working/3D/935' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(OC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498047.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498047.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498047/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498047 none CCCC(OC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 190, 164, 125, 164, 164, 125, 125, 81, 81, 81, 81, 81, 57, 35, 57, 13, 1, 1, 1, 1, 1, 1, 1, 81, 201, 201, 201, 201, 201, 201, 201, 164, 164, 164, 164, 125, 81, 81, 81, 81, 81, 35, 35, 1, 81, 81] 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])
total number of confs: 900
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: REAL300025498047 none CCCC(OC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 12, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [25, 23, 11, 5, 11, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 16, 81, 81, 81, 81, 81, 1, 25, 25, 25, 25, 25, 25, 25, 11, 12, 12, 12, 5, 1, 1, 1, 1, 1, 8, 8, 81, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 235
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498047 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498047
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498047/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498047
Building REAL300025498048
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498048'
/scratch/stefan/7787277/working/building/REAL300025498048 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498048

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498048/0 /scratch/stefan/7787277/working/building/REAL300025498048 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 936)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/936
`/scratch/stefan/7787277/working/3D/936' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=C(C)C(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498048.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498048.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498048/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498048 none C=C(C)C(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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
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, 8, 9, 9, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 5, 1, 1, 1, 1, 1, 1, 1, 6, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 6, 6, 6, 6, 6, 6, 6, 1, 6, 6] 9
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])
total number of confs: 24
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: REAL300025498048 none C=C(C)C(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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
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, 6, 7, 7, 6, 6, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 6, 6, 6, 6, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 1, 1, 1, 1, 1, 5, 5, 6, 1, 1] 9
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 35
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498048 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498048
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498048/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498048
Building REAL300025498049
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498049'
/scratch/stefan/7787277/working/building/REAL300025498049 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498049

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498049/0 /scratch/stefan/7787277/working/building/REAL300025498049 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 937)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/937
`/scratch/stefan/7787277/working/3D/937' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CN1CCNC(=O)C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498049.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498049.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498049/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498049 none O=C(CN1CCNC(=O)C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 10, 5, 5, 8, 1, 11, 5, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 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: [5, 5, 5, 13, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 6, 6, 18, 35, 110, 110, 110, 110, 110, 1, 13, 13, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 18, 18, 110, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 240
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498049 none O=C(CN1CCNC(=O)C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 10, 5, 5, 8, 1, 11, 5, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 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: [146, 146, 146, 201, 201, 201, 201, 201, 201, 201, 110, 110, 110, 110, 110, 65, 31, 65, 13, 1, 1, 1, 1, 1, 1, 1, 110, 201, 201, 201, 201, 201, 201, 201, 201, 201, 146, 110, 110, 110, 110, 110, 31, 31, 1, 110, 110] 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])
total number of confs: 740
number of broken/clashed sets: 59
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498049 none O=C(CN1CCNC(=O)C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 10, 5, 5, 8, 1, 11, 5, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 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: [8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 14, 14, 14, 14, 14, 39, 39, 73, 114, 201, 201, 201, 201, 201, 14, 4, 4, 1, 1, 1, 1, 1, 1, 1, 8, 14, 14, 14, 14, 14, 73, 73, 201, 14, 14] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 487
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498049 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498049
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498049/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498049
Building REAL300025498050
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498050'
/scratch/stefan/7787277/working/building/REAL300025498050 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498050

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498050/0 /scratch/stefan/7787277/working/building/REAL300025498050 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 938)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/938
`/scratch/stefan/7787277/working/3D/938' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(CC(N)=O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498050.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498050.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498050/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498050 none CC(CC(N)=O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 151, 199, 201, 201, 201, 151, 151, 113, 113, 113, 113, 113, 70, 31, 70, 13, 1, 1, 1, 1, 1, 1, 1, 113, 199, 199, 199, 199, 201, 201, 201, 201, 151, 113, 113, 113, 113, 113, 31, 31, 1, 113, 113] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43])
total number of confs: 710
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: REAL300025498050 none CC(CC(N)=O)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 1, 8, 11, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 5, 14, 20, 35, 35, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 27, 113, 113, 113, 113, 113, 1, 14, 14, 14, 14, 20, 20, 35, 35, 5, 1, 1, 1, 1, 1, 15, 15, 113, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 309
number of broken/clashed sets: 83
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498050 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498050
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498050/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498050
Building REAL300025498051
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498051'
/scratch/stefan/7787277/working/building/REAL300025498051 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498051

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498051/0 /scratch/stefan/7787277/working/building/REAL300025498051 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 939)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/939
`/scratch/stefan/7787277/working/3D/939' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1CCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498051.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498051.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498051/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498051 none NC(=O)C1CCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 21, 41, 21, 21, 21, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 27, 92, 92, 92, 92, 92, 1, 41, 41, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 16, 16, 92, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 43, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 262
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498051 none NC(=O)C1CCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 140, 140, 140, 92, 92, 92, 92, 92, 68, 31, 68, 13, 1, 1, 1, 1, 1, 1, 1, 92, 201, 201, 201, 201, 201, 201, 201, 201, 140, 92, 92, 92, 92, 92, 31, 31, 1, 92, 92] 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])
total number of confs: 626
number of broken/clashed sets: 43
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498051 none NC(=O)C1CCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 10, 10, 10, 21, 21, 21, 21, 21, 28, 28, 62, 103, 201, 201, 201, 201, 201, 21, 8, 8, 1, 1, 1, 1, 1, 1, 10, 21, 21, 21, 21, 21, 62, 62, 201, 21, 21] 201
rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 33, 28, 29, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 475
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498051 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498051
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498051/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498051
Building REAL300025498052
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498052'
/scratch/stefan/7787277/working/building/REAL300025498052 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498052

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498052/0 /scratch/stefan/7787277/working/building/REAL300025498052 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 940)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/940
`/scratch/stefan/7787277/working/3D/940' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCNC2=O)C1)

`REAL300025498052.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498052.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498052/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498052 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCNC2=O)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 36, 126, 126, 126, 126, 126, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 1, 16, 16, 126, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 15, 1, 1] 201
rigid atoms, others: [32, 1, 40, 41, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 247
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498052 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCNC2=O)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 15, 42, 79, 122, 201, 201, 201, 201, 201, 15, 15, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 15, 79, 79, 201, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 1, 1, 15, 15] 201
rigid atoms, others: [34, 35, 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, 40, 41])
total number of confs: 507
number of broken/clashed sets: 32
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498052 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CCNC2=O)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.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']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 46, 13, 1, 1, 1, 1, 1, 1, 1, 95, 126, 126, 126, 126, 126, 154, 154, 154, 201, 201, 201, 201, 201, 126, 46, 46, 1, 126, 126, 126, 126, 126, 154, 201, 201, 201, 201, 201, 201, 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, 41])
total number of confs: 635
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498052 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498052
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498052/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498052
Building REAL300025498053
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498053'
/scratch/stefan/7787277/working/building/REAL300025498053 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498053

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498053/0 /scratch/stefan/7787277/working/building/REAL300025498053 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 941)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/941
`/scratch/stefan/7787277/working/3D/941' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498053.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498053.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498053/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498053 none CN1C(=O)NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 23, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 35, 122, 122, 122, 122, 122, 1, 23, 23, 23, 23, 23, 4, 1, 1, 1, 1, 1, 15, 15, 122, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 228
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498053 none CN1C(=O)NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 153, 153, 153, 122, 122, 122, 122, 122, 110, 55, 110, 13, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 201, 153, 122, 122, 122, 122, 122, 55, 55, 1, 122, 122] 201
rigid atoms, others: [39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41])
total number of confs: 578
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498053 none CN1C(=O)NC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 23, 23, 23, 23, 23, 45, 45, 75, 126, 201, 201, 201, 201, 201, 23, 2, 2, 2, 1, 1, 9, 23, 23, 23, 23, 23, 75, 75, 201, 23, 23] 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])
total number of confs: 473
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498053 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498053
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498053/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498053
Building REAL300025498054
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498054'
/scratch/stefan/7787277/working/building/REAL300025498054 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498054

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498054/0 /scratch/stefan/7787277/working/building/REAL300025498054 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 942)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/942
`/scratch/stefan/7787277/working/3D/942' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)NC1=O)

`REAL300025498054.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498054.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498054/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498054 none CN1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [21, 21, 21, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 43, 132, 132, 132, 132, 132, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 4, 1, 1, 1, 1, 1, 24, 24, 132, 1, 1, 21] 201
rigid atoms, others: [33, 34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 22, 41, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43])
total number of confs: 287
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498054 none CN1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 166, 166, 166, 132, 132, 132, 132, 132, 108, 43, 108, 13, 1, 1, 1, 1, 1, 1, 1, 132, 201, 201, 201, 201, 201, 201, 201, 201, 201, 166, 132, 132, 132, 132, 132, 43, 43, 1, 132, 132, 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])
total number of confs: 630
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498054 none CN1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.am', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 10, 21, 21, 21, 21, 21, 48, 48, 103, 138, 201, 201, 201, 201, 201, 21, 1, 1, 1, 2, 2, 2, 1, 1, 1, 10, 21, 21, 21, 21, 21, 103, 103, 201, 21, 21, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 43, 23, 24, 25, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 577
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498054 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498054
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498054/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498054
Building REAL300025498055
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498055'
/scratch/stefan/7787277/working/building/REAL300025498055 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498055

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498055/0 /scratch/stefan/7787277/working/building/REAL300025498055 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 943)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/943
`/scratch/stefan/7787277/working/3D/943' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498055.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498055.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498055/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498055 none C=CC(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 108, 201, 201, 108, 108, 71, 71, 71, 71, 71, 57, 43, 57, 13, 1, 1, 1, 1, 1, 1, 1, 71, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 71, 71, 71, 71, 71, 43, 43, 1, 71, 71] 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])
total number of confs: 844
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: REAL300025498055 none C=CC(C)(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [22, 14, 5, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 20, 71, 71, 71, 71, 71, 1, 22, 22, 22, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 11, 11, 71, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 43, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 203
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498055 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498055
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498055/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498055
Building REAL300025498056
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498056'
/scratch/stefan/7787277/working/building/REAL300025498056 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498056

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498056/0 /scratch/stefan/7787277/working/building/REAL300025498056 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 944)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/944
`/scratch/stefan/7787277/working/3D/944' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C#CCCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498056.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498056.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498056/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498056 none C#CCCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 201, 148, 155, 148, 131, 46, 46, 46, 37, 37, 37, 37, 37, 36, 27, 36, 12, 1, 1, 1, 1, 1, 1, 1, 37, 201, 194, 201, 155, 155, 155, 155, 155, 155, 131, 131, 46, 37, 37, 37, 37, 37, 27, 27, 1, 37, 37] 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])
total number of confs: 971
number of broken/clashed sets: 40
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498056 none C#CCCCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [37, 37, 19, 21, 19, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 37, 37, 37, 37, 37, 1, 37, 37, 38, 21, 21, 21, 21, 21, 21, 14, 14, 3, 1, 1, 1, 1, 1, 5, 5, 37, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 241
number of broken/clashed sets: 40
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498056 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498056
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498056/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498056
Building REAL300025498057
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498057'
/scratch/stefan/7787277/working/building/REAL300025498057 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
3 protomers extracted for REAL300025498057

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498057/0 /scratch/stefan/7787277/working/building/REAL300025498057 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 945)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/945
`/scratch/stefan/7787277/working/3D/945' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@@H+]1CCC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498057.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498057.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498057/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498057 none C[N@@H+]1CCC[C@@H]1C(=O)NC1C=CCN(C(=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', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
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: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 40, 93, 93, 93, 93, 93, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 24, 24, 93, 1, 1] 110
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 202
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498057 none C[N@@H+]1CCC[C@@H]1C(=O)NC1C=CCN(C(=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', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 93, 93, 93, 93, 93, 76, 47, 76, 12, 1, 1, 1, 1, 1, 1, 1, 93, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 93, 93, 93, 93, 93, 47, 47, 1, 93, 93] 110
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])
total number of confs: 355
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498057 none C[N@@H+]1CCC[C@@H]1C(=O)NC1C=CCN(C(=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', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
110  conformations in input
total number of sets (complete confs): 110
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 17, 17, 39, 59, 110, 110, 110, 110, 110, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 39, 39, 110, 5, 5] 110
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 35, 33, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 266
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498057 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025498057/1 /scratch/stefan/7787277/working/building/REAL300025498057 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 946)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/946
`/scratch/stefan/7787277/working/3D/946' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[N@H+]1CCC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498057.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025498057.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498057/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498057 none C[N@H+]1CCC[C@@H]1C(=O)NC1C=CCN(C(=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', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [7, 7, 7, 7, 7, 7, 5, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 34, 109, 109, 109, 109, 109, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 1, 1, 1, 1, 1, 18, 18, 109, 1, 1] 135
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 212
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498057 none C[N@H+]1CCC[C@@H]1C(=O)NC1C=CCN(C(=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', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [135, 135, 135, 135, 135, 135, 135, 135, 135, 135, 109, 109, 109, 109, 109, 100, 60, 100, 12, 1, 1, 1, 1, 1, 1, 1, 109, 135, 135, 135, 135, 135, 135, 135, 135, 135, 135, 109, 109, 109, 109, 109, 60, 60, 1, 109, 109] 135
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])
total number of confs: 453
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498057 none C[N@H+]1CCC[C@@H]1C(=O)NC1C=CCN(C(=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', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 9, 6, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
135  conformations in input
total number of sets (complete confs): 135
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 18, 18, 42, 71, 135, 135, 135, 135, 135, 7, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 7, 7, 7, 7, 7, 42, 42, 135, 7, 7] 135
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 35, 33, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 325
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498057 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `2'
/scratch/stefan/7787277/working/building/REAL300025498057/2 /scratch/stefan/7787277/working/building/REAL300025498057 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 2 (index: 947)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/947
`/scratch/stefan/7787277/working/3D/947' -> `2.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498057.mol2' -> `2.mol2'
`temp.mol2' -> `REAL300025498057.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498057/2/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: REAL300025498057 none CN1CCC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 59, 162, 162, 162, 162, 162, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 22, 22, 162, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 294
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498057 none CN1CCC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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, 201, 201, 201, 201, 201, 201, 201, 201, 162, 161, 161, 161, 161, 124, 56, 124, 12, 1, 1, 1, 1, 1, 1, 1, 161, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 162, 162, 162, 162, 56, 56, 1, 161, 161] 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])
total number of confs: 622
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498057 none CN1CCC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 10, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 23, 23, 56, 102, 201, 201, 201, 201, 201, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 56, 56, 201, 5, 5] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 7, 34, 33, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 440
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498057 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498057
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498057/0.*
1: /scratch/stefan/7787277/working/building/REAL300025498057/1.*
2: /scratch/stefan/7787277/working/building/REAL300025498057/2.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498057
Building REAL300025498058
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498058'
/scratch/stefan/7787277/working/building/REAL300025498058 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498058

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498058/0 /scratch/stefan/7787277/working/building/REAL300025498058 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 948)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/948
`/scratch/stefan/7787277/working/3D/948' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@@H]1C[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498058.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498058.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498058/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498058 none C[C@@H]1C[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 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, 6, 7, 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: [22, 22, 22, 22, 5, 22, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 28, 91, 91, 91, 91, 91, 1, 22, 22, 22, 22, 22, 5, 1, 1, 1, 1, 1, 13, 13, 91, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 201
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498058 none C[C@@H]1C[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 116, 201, 116, 116, 91, 91, 91, 91, 91, 80, 35, 80, 12, 1, 1, 1, 1, 1, 1, 1, 91, 201, 201, 201, 201, 201, 116, 91, 91, 91, 91, 91, 35, 35, 1, 91, 91] 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])
total number of confs: 653
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498058 none C[C@@H]1C[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 22, 22, 22, 22, 22, 44, 44, 83, 114, 201, 201, 201, 201, 201, 22, 2, 2, 2, 1, 1, 11, 22, 22, 22, 22, 22, 83, 83, 201, 22, 22] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 523
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498058 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498058
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498058/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498058
Building REAL300025498059
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498059'
/scratch/stefan/7787277/working/building/REAL300025498059 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498059

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498059/0 /scratch/stefan/7787277/working/building/REAL300025498059 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 949)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/949
`/scratch/stefan/7787277/working/3D/949' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1CC=CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498059.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498059.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498059/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498059 none O=C(CC1CC=CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 25, 43, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 53, 53, 53, 53, 53, 1, 25, 25, 43, 43, 43, 43, 43, 43, 43, 43, 43, 5, 1, 1, 1, 1, 1, 6, 6, 53, 1, 1] 201
rigid atoms, others: [38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 46, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 223
number of broken/clashed sets: 58
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498059 none O=C(CC1CC=CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [84, 84, 84, 189, 201, 201, 201, 201, 201, 53, 53, 53, 53, 53, 44, 28, 44, 12, 1, 1, 1, 1, 1, 1, 1, 53, 189, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 84, 53, 53, 53, 53, 53, 28, 28, 1, 53, 53] 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])
total number of confs: 798
number of broken/clashed sets: 58
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498059 none O=C(CC1CC=CCC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 1, 1, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 43, 43, 43, 43, 43, 52, 52, 88, 132, 201, 201, 201, 201, 201, 43, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 43, 43, 43, 43, 43, 88, 88, 201, 43, 43] 201
rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35, 36, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 546
number of broken/clashed sets: 58
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498059 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498059
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498059/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498059
Building REAL300025498060
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498060'
/scratch/stefan/7787277/working/building/REAL300025498060 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498060

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498060/0 /scratch/stefan/7787277/working/building/REAL300025498060 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 950)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/950
`/scratch/stefan/7787277/working/3D/950' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1)

`REAL300025498060.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498060.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498060/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498060 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens 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, 4, 4, 11, 22, 74, 74, 74, 74, 74, 1, 19, 19, 19, 19, 19, 19, 4, 1, 1, 1, 1, 1, 11, 11, 74, 1, 1, 19, 19, 19, 19, 19, 19] 201
rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 10, 37, 20, 36, 28, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 33, 34, 35, 38, 39, 40, 41, 42, 43])
total number of confs: 168
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498060 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens need 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, 74, 74, 74, 74, 74, 66, 43, 66, 13, 1, 1, 1, 1, 1, 1, 1, 74, 201, 201, 201, 201, 201, 201, 99, 74, 74, 74, 74, 74, 43, 43, 1, 74, 74, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [35, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 658
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498060 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens need rotated
201  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, 39, 39, 61, 97, 201, 201, 201, 201, 201, 19, 1, 1, 1, 2, 2, 2, 7, 19, 19, 19, 19, 19, 61, 61, 201, 19, 19, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 38, 39, 40, 41, 42, 43, 21, 22, 23] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 456
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498060 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498060
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498060/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498060
Building REAL300025498061
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498061'
/scratch/stefan/7787277/working/building/REAL300025498061 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498061

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498061/0 /scratch/stefan/7787277/working/building/REAL300025498061 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 951)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/951
`/scratch/stefan/7787277/working/3D/951' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(C[C@@H]1C[C@H]1C1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498061.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498061.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498061/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025498061 none O=C(C[C@@H]1C[C@H]1C1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 16, 5, 5, 5, 5, 1, 5, 1, 1, 1, 56, 56, 56, 56, 56, 56, 56, 57, 57, 105, 128, 201, 201, 201, 201, 201, 56, 16, 16, 5, 5, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 56, 105, 105, 201, 56, 56] 201
rigid atoms, others: [32, 33, 34, 35, 36, 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, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 569
number of broken/clashed sets: 81
./output.2.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: REAL300025498061 none O=C(C[C@@H]1C[C@H]1C1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [80, 80, 80, 152, 197, 197, 197, 197, 197, 201, 201, 60, 60, 60, 60, 60, 52, 24, 52, 12, 1, 1, 1, 1, 1, 1, 1, 60, 152, 152, 197, 197, 201, 201, 201, 201, 201, 80, 60, 60, 60, 60, 60, 24, 24, 1, 60, 60] 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, 46, 47])
total number of confs: 718
number of broken/clashed sets: 81
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498061 none O=C(C[C@@H]1C[C@H]1C1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need 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, 14, 36, 36, 36, 36, 36, 56, 56, 1, 1, 1, 1, 1, 1, 1, 2, 2, 10, 20, 60, 60, 60, 60, 60, 1, 14, 14, 36, 36, 56, 56, 56, 56, 56, 3, 1, 1, 1, 1, 1, 10, 10, 60, 1, 1] 201
rigid atoms, others: [47, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 287
number of broken/clashed sets: 81
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498061 none O=C(C[C@@H]1C[C@H]1C1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 7, 5, 5, 7, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [36, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 36, 36, 36, 36, 36, 36, 36, 37, 37, 81, 107, 197, 197, 197, 197, 197, 36, 7, 7, 1, 1, 5, 5, 5, 5, 5, 36, 36, 36, 36, 36, 36, 81, 81, 197, 36, 36] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 514
number of broken/clashed sets: 81
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498061 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498061
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498061/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498061
Building REAL300025498062
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498062'
/scratch/stefan/7787277/working/building/REAL300025498062 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498062

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498062/0 /scratch/stefan/7787277/working/building/REAL300025498062 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 952)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/952
`/scratch/stefan/7787277/working/3D/952' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1COC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025498062.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498062.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498062/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498062 none CC1COC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 1, 1, 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, 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, 7]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 48, 133, 133, 133, 133, 133, 1, 20, 20, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 26, 26, 133, 1, 1, 20, 20] 201
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40, 43, 44])
total number of confs: 290
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498062 none CC1COC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 1, 1, 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, 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, 7]
0  hydrogens need rotated
201  conformations 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, 133, 133, 133, 133, 133, 100, 42, 100, 13, 1, 1, 1, 1, 1, 1, 1, 133, 201, 201, 201, 201, 201, 201, 201, 201, 168, 133, 133, 133, 133, 133, 42, 42, 1, 133, 133, 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])
total number of confs: 624
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498062 none CC1COC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', '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, 1, 1, 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, 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, 7]
0  hydrogens need rotated
201  conformations in input
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, 20, 20, 20, 20, 20, 43, 43, 104, 139, 201, 201, 201, 201, 201, 20, 1, 2, 2, 2, 1, 1, 1, 1, 9, 20, 20, 20, 20, 20, 104, 104, 201, 20, 20, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 44, 24, 28, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 576
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498062 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498062
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498062/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498062
Building REAL300025498063
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498063'
/scratch/stefan/7787277/working/building/REAL300025498063 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498063

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498063/0 /scratch/stefan/7787277/working/building/REAL300025498063 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 953)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/953
`/scratch/stefan/7787277/working/3D/953' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=CC1=O)

`REAL300025498063.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498063.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498063/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498063 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 11, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [10, 10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 55, 143, 143, 143, 143, 143, 1, 10, 10, 10, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 1, 33, 32, 143, 1, 1, 10] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42])
total number of confs: 299
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498063 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 11, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 143, 143, 143, 143, 143, 108, 44, 108, 13, 1, 1, 1, 1, 1, 1, 1, 143, 201, 201, 201, 201, 201, 201, 201, 201, 201, 143, 143, 143, 143, 143, 44, 44, 1, 143, 143, 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])
total number of confs: 605
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498063 none CN1C=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=CC1=O NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 1, 11, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 29, 29, 85, 123, 201, 201, 201, 201, 201, 10, 1, 1, 1, 1, 2, 2, 2, 1, 4, 10, 10, 10, 10, 10, 85, 85, 201, 10, 10, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 42, 23, 24, 25, 26, 30] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 527
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498063 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498063
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498063/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498063
Building REAL300025498064
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498064'
/scratch/stefan/7787277/working/building/REAL300025498064 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498064

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498064/0 /scratch/stefan/7787277/working/building/REAL300025498064 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 954)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/954
`/scratch/stefan/7787277/working/3D/954' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@]23C[C@H]2CCC3)C1)

`REAL300025498064.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498064.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498064/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498064 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@]23C[C@H]2CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 6, 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, 13, 29, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 1, 13, 13, 78, 1, 1, 1, 1, 1, 4, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1] 201
rigid atoms, others: [32, 1, 43, 33, 44, 10, 11, 12, 13, 14, 15, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 159
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498064 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@]23C[C@H]2CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 6, 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: [29, 15, 29, 68, 108, 201, 201, 201, 201, 201, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 15, 68, 68, 201, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 201
rigid atoms, others: [35, 36, 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, 43, 44])
total number of confs: 485
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498064 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@]23C[C@H]2CCC3)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 6, 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: [64, 35, 13, 1, 1, 1, 1, 1, 1, 1, 64, 78, 78, 78, 78, 78, 101, 101, 101, 201, 201, 201, 201, 201, 201, 78, 35, 35, 1, 78, 78, 78, 78, 78, 101, 201, 201, 201, 201, 201, 201, 201, 201, 78, 78] 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: 491
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498064 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498064
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498064/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498064
Building REAL300025498065
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498065'
/scratch/stefan/7787277/working/building/REAL300025498065 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498065

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498065/0 /scratch/stefan/7787277/working/building/REAL300025498065 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 955)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/955
`/scratch/stefan/7787277/working/3D/955' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2CCO[C@H]2C2CC2)C1)

`REAL300025498065.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498065.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498065/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window 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: REAL300025498065 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2CCO[C@H]2C2CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 5, 7, 7, 6, 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, 7]
0  hydrogens 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, 8, 13, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 4, 4, 4, 15, 15, 15, 15, 15, 15, 15, 27, 27, 1, 8, 8, 47, 1, 1, 1, 1, 1, 4, 15, 15, 15, 15, 27, 27, 27, 27, 27, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 36, 33, 10, 11, 12, 13, 14, 15, 48, 47, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 165
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.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: REAL300025498065 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2CCO[C@H]2C2CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 5, 7, 7, 6, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [49, 27, 49, 76, 104, 201, 201, 201, 201, 201, 27, 27, 27, 27, 13, 13, 4, 13, 4, 4, 4, 4, 4, 1, 4, 1, 1, 1, 27, 76, 76, 201, 27, 27, 27, 27, 27, 13, 4, 4, 4, 4, 1, 1, 1, 1, 1, 27, 27] 201
rigid atoms, others: [42, 43, 44, 45, 46, 23, 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, 21, 22, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48])
total number of confs: 507
number of broken/clashed sets: 13
./output.4.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498065 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2CCO[C@H]2C2CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 5, 7, 7, 6, 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, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [35, 15, 35, 58, 80, 183, 183, 183, 183, 183, 15, 15, 15, 15, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 15, 58, 58, 183, 15, 15, 15, 15, 15, 7, 1, 1, 1, 1, 4, 4, 4, 4, 4, 15, 15] 201
rigid atoms, others: [38, 39, 40, 41, 16, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 431
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498065 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2CCO[C@H]2C2CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 12, 5, 7, 5, 5, 5, 5, 7, 7, 6, 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, 7]
0  hydrogens 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, 12, 1, 1, 1, 1, 1, 1, 1, 34, 47, 47, 47, 47, 47, 82, 82, 82, 183, 183, 183, 183, 183, 183, 183, 201, 201, 47, 23, 23, 1, 47, 47, 47, 47, 47, 82, 183, 183, 183, 183, 201, 201, 201, 201, 201, 47, 47] 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])
total number of confs: 634
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498065 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498065
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498065/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498065
Building REAL300025498066
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498066'
/scratch/stefan/7787277/working/building/REAL300025498066 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498066

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498066/0 /scratch/stefan/7787277/working/building/REAL300025498066 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 956)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/956
`/scratch/stefan/7787277/working/3D/956' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[C@@H]1OCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498066.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498066.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498066/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498066 none CC[C@@H]1OCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [23, 21, 21, 21, 21, 21, 21, 5, 21, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 37, 104, 104, 104, 104, 104, 1, 23, 23, 23, 23, 23, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 22, 22, 104, 1, 1] 201
rigid atoms, others: [47, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 46, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 256
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498066 none CC[C@@H]1OCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 148, 201, 148, 148, 104, 104, 104, 104, 104, 88, 41, 88, 12, 1, 1, 1, 1, 1, 1, 1, 104, 201, 201, 201, 201, 201, 201, 201, 201, 201, 148, 104, 104, 104, 104, 104, 41, 41, 1, 104, 104] 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, 46, 47])
total number of confs: 656
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498066 none CC[C@@H]1OCC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 7, 12, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 21, 21, 21, 21, 21, 57, 57, 112, 141, 201, 201, 201, 201, 201, 21, 3, 3, 3, 3, 3, 1, 1, 1, 1, 8, 21, 21, 21, 21, 21, 112, 112, 201, 21, 21] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 34, 35, 36, 33] set([0, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 572
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498066 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498066
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498066/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498066
Building REAL300025498067
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498067'
/scratch/stefan/7787277/working/building/REAL300025498067 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498067

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498067/0 /scratch/stefan/7787277/working/building/REAL300025498067 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 957)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/957
`/scratch/stefan/7787277/working/3D/957' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)=C1)

`REAL300025498067.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498067.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498067/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498067 none CC1=CN=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)=C1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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]
0  hydrogens 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, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 43, 115, 115, 115, 115, 115, 1, 15, 15, 15, 15, 15, 15, 15, 4, 1, 1, 1, 1, 1, 24, 24, 115, 1, 1, 15, 15, 15, 15] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45])
total number of confs: 250
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498067 none CC1=CN=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)=C1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 161, 161, 161, 115, 115, 115, 115, 115, 84, 38, 84, 13, 1, 1, 1, 1, 1, 1, 1, 115, 201, 201, 201, 201, 201, 201, 201, 161, 115, 115, 115, 115, 115, 38, 38, 1, 115, 115, 201, 201, 201, 201] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45])
total number of confs: 575
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498067 none CC1=CN=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)=C1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
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, 15, 15, 15, 15, 15, 39, 39, 98, 136, 201, 201, 201, 201, 201, 15, 1, 1, 1, 2, 2, 2, 1, 7, 15, 15, 15, 15, 15, 98, 98, 201, 15, 15, 2, 2, 2, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 24, 25, 26, 30] set([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])
total number of confs: 576
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498067 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498067
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498067/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498067
Building REAL300025498068
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498068'
/scratch/stefan/7787277/working/building/REAL300025498068 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498068

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498068/0 /scratch/stefan/7787277/working/building/REAL300025498068 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 958)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/958
`/scratch/stefan/7787277/working/3D/958' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CN=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1C)

`REAL300025498068.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498068.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498068/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498068 none CC1=CN=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1C 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 54, 145, 145, 145, 145, 145, 1, 10, 10, 10, 10, 10, 10, 10, 5, 1, 1, 1, 1, 1, 32, 32, 145, 1, 1, 10, 10, 10, 10] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45])
total number of confs: 300
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498068 none CC1=CN=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1C 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations 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, 145, 145, 145, 145, 145, 105, 43, 105, 13, 1, 1, 1, 1, 1, 1, 1, 145, 201, 201, 201, 201, 201, 201, 201, 200, 145, 145, 145, 145, 145, 43, 43, 1, 145, 145, 201, 201, 201, 201] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45])
total number of confs: 602
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498068 none CC1=CN=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=C1C 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
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, 10, 10, 10, 10, 10, 31, 31, 86, 122, 201, 201, 201, 201, 201, 10, 1, 1, 1, 2, 2, 2, 1, 3, 10, 10, 10, 10, 10, 86, 86, 201, 10, 10, 1, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 24, 25, 26, 30] set([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, 43, 44, 45])
total number of confs: 533
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498068 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498068
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498068/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498068
Building REAL300025498069
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498069'
/scratch/stefan/7787277/working/building/REAL300025498069 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498069

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498069/0 /scratch/stefan/7787277/working/building/REAL300025498069 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 959)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/959
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2CC[C@@H]3C[C@@H]3CC2)C1)

`REAL300025498069.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498069.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498069/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498069 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC[C@@H]3C[C@@H]3CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 6, 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, 7]
0  hydrogens 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, 20, 37, 89, 89, 89, 89, 89, 1, 1, 1, 1, 1, 1, 5, 5, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 20, 20, 89, 1, 1, 1, 1, 1, 5, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 36, 33, 10, 11, 12, 13, 14, 15, 49, 50, 28] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 225
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498069 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC[C@@H]3C[C@@H]3CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 6, 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, 7]
0  hydrogens 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, 21, 51, 103, 136, 201, 201, 201, 201, 201, 21, 21, 21, 21, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 103, 103, 201, 21, 21, 21, 21, 21, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 201
rigid atoms, others: [16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 49, 50])
total number of confs: 571
number of broken/clashed sets: 201
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498069 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC[C@@H]3C[C@@H]3CC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', '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', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 6, 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, 7]
0  hydrogens 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, 37, 13, 1, 1, 1, 1, 1, 1, 1, 76, 89, 89, 89, 89, 89, 118, 118, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 37, 37, 1, 89, 89, 89, 89, 89, 118, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 89] 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: 656
number of broken/clashed sets: 201
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498069 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498069
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498069/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498069
Building REAL300025498070
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498070'
/scratch/stefan/7787277/working/building/REAL300025498070 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498070

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498070/0 /scratch/stefan/7787277/working/building/REAL300025498070 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 960)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/960
`/scratch/stefan/7787277/working/3D/960' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1C=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1)

`REAL300025498070.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498070.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498070/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498070 none CCN1C=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.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, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 11, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 13, 63, 63, 63, 63, 63, 1, 11, 11, 21, 21, 21, 21, 21, 11, 11, 11, 3, 1, 1, 1, 1, 1, 7, 7, 63, 1, 1] 201
rigid atoms, others: [45, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 40, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43])
total number of confs: 190
number of broken/clashed sets: 90
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498070 none CCN1C=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.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, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 119, 119, 119, 119, 67, 67, 67, 63, 63, 63, 63, 63, 47, 29, 47, 13, 1, 1, 1, 1, 1, 1, 1, 63, 119, 119, 201, 201, 201, 201, 201, 119, 119, 119, 67, 63, 63, 63, 63, 63, 29, 29, 1, 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])
total number of confs: 967
number of broken/clashed sets: 90
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498070 none CCN1C=C(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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.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, 8, 1, 1, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 3, 8, 8, 8, 11, 11, 11, 11, 11, 16, 16, 33, 56, 119, 119, 119, 119, 119, 11, 1, 1, 4, 4, 4, 4, 4, 1, 3, 3, 8, 11, 11, 11, 11, 11, 33, 33, 119, 11, 11] 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: 285
number of broken/clashed sets: 90
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498070 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498070
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498070/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498070
Building REAL300025498071
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498071'
/scratch/stefan/7787277/working/building/REAL300025498071 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498071

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498071/0 /scratch/stefan/7787277/working/building/REAL300025498071 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 961)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/961
`/scratch/stefan/7787277/working/3D/961' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC2CC2CC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498071.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498071.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498071/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498071 none CC1CC2CC2CC1C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 35, 96, 96, 96, 96, 96, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 20, 20, 96, 1, 1] 201
rigid atoms, others: [45, 43, 41, 10, 11, 12, 13, 14, 15, 16, 49, 44, 50, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 46, 47, 48])
total number of confs: 223
number of broken/clashed sets: 20
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498071 none CC1CC2CC2CC1C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
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, 129, 129, 129, 96, 96, 96, 96, 96, 75, 37, 75, 13, 1, 1, 1, 1, 1, 1, 1, 96, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 96, 96, 96, 96, 96, 37, 37, 1, 96, 96] 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, 50])
total number of confs: 697
number of broken/clashed sets: 20
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498071 none CC1CC2CC2CC1C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 43, 43, 86, 122, 201, 201, 201, 201, 201, 13, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 13, 13, 13, 13, 13, 86, 86, 201, 13, 13] 201
rigid atoms, others: [0, 1, 2, 3, 32, 5, 6, 7, 8, 39, 34, 35, 4, 33, 38, 36, 37, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 534
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498071 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498071
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498071/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498071
Building REAL300025498072
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498072'
/scratch/stefan/7787277/working/building/REAL300025498072 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498072

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498072/0 /scratch/stefan/7787277/working/building/REAL300025498072 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 962)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/962
`/scratch/stefan/7787277/working/3D/962' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=CN=C1CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498072.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498072.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498072/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498072 none CN1C=CN=C1CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [16, 16, 16, 16, 16, 16, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 41, 133, 133, 133, 133, 133, 1, 16, 16, 16, 16, 16, 16, 16, 15, 15, 5, 1, 1, 1, 1, 1, 23, 23, 133, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 297
number of broken/clashed sets: 56
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498072 none CN1C=CN=C1CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 162, 162, 162, 133, 133, 133, 133, 133, 78, 30, 78, 13, 1, 1, 1, 1, 1, 1, 1, 133, 201, 201, 201, 201, 201, 201, 201, 201, 201, 162, 133, 133, 133, 133, 133, 30, 30, 1, 133, 133] 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])
total number of confs: 634
number of broken/clashed sets: 56
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498072 none CN1C=CN=C1CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 1, 8, 1, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total 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, 8, 8, 8, 16, 16, 16, 16, 16, 36, 36, 74, 116, 201, 201, 201, 201, 201, 16, 2, 2, 2, 1, 1, 4, 4, 4, 4, 8, 16, 16, 16, 16, 16, 74, 74, 201, 16, 16] 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: 516
number of broken/clashed sets: 56
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498072 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498072
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498072/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498072
Building REAL300025498073
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498073'
/scratch/stefan/7787277/working/building/REAL300025498073 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498073

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498073/0 /scratch/stefan/7787277/working/building/REAL300025498073 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 963)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/963
`/scratch/stefan/7787277/working/3D/963' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@@H]3CCCC[C@H]23)C1)

`REAL300025498073.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498073.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498073/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498073 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@@H]3CCCC[C@H]23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', '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, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 6, 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: [7, 1, 7, 24, 39, 108, 108, 108, 108, 108, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 24, 24, 108, 1, 1, 1, 1, 1, 5, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1] 201
rigid atoms, others: [1, 34, 35, 36, 37, 33, 10, 11, 12, 13, 14, 15, 49, 50, 29] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48])
total number of confs: 246
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498073 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@@H]3CCCC[C@H]23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', '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, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 6, 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, 15, 42, 95, 130, 201, 201, 201, 201, 201, 15, 15, 15, 15, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 95, 95, 201, 15, 15, 15, 15, 15, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 201
rigid atoms, others: [16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49, 50])
total number of confs: 545
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498073 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@@H]2C[C@@H]3CCCC[C@H]23)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', '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, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 5, 5, 5, 7, 5, 7, 7, 6, 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: [94, 44, 12, 1, 1, 1, 1, 1, 1, 1, 94, 108, 108, 108, 108, 108, 147, 147, 147, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 44, 44, 1, 108, 108, 108, 108, 108, 147, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 108, 108] 201
rigid atoms, others: [32, 3, 4, 5, 6, 7, 8, 9] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 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: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498073 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498073
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498073/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498073
Building REAL300025498074
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498074'
/scratch/stefan/7787277/working/building/REAL300025498074 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498074

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498074/0 /scratch/stefan/7787277/working/building/REAL300025498074 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 964)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/964
`/scratch/stefan/7787277/working/3D/964' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H](CC(F)(F)F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498074.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498074.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498074/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498074 none C[C@H](CC(F)(F)F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 7, 5, 5, 15, 15, 15, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens 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, 137, 189, 189, 201, 201, 201, 201, 137, 137, 84, 84, 84, 84, 84, 68, 50, 68, 13, 1, 1, 1, 1, 1, 1, 1, 84, 189, 189, 189, 201, 201, 137, 84, 84, 84, 84, 84, 50, 50, 1, 84, 84] 201
rigid atoms, others: [40, 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, 41, 42])
total number of confs: 793
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: REAL300025498074 none C[C@H](CC(F)(F)F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'F', 'F', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 7, 5, 5, 15, 15, 15, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens 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, 18, 18, 28, 28, 28, 28, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 84, 84, 84, 84, 84, 1, 18, 18, 18, 28, 28, 5, 1, 1, 1, 1, 1, 10, 10, 84, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 41, 10, 11, 12, 13, 14, 15, 16, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 245
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498074 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498074
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498074/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498074
Building REAL300025498075
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498075'
/scratch/stefan/7787277/working/building/REAL300025498075 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498075

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498075/0 /scratch/stefan/7787277/working/building/REAL300025498075 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 965)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/965
`/scratch/stefan/7787277/working/3D/965' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: COC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCC1)

`REAL300025498075.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498075.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498075/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498075 none COC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 7, 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: [162, 162, 158, 158, 158, 108, 108, 108, 108, 108, 77, 38, 77, 13, 1, 1, 1, 1, 1, 1, 1, 108, 162, 201, 201, 201, 201, 162, 162, 162, 162, 158, 108, 108, 108, 108, 108, 38, 38, 1, 108, 108, 201, 201, 201, 201, 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, 48, 49, 50])
total number of confs: 674
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498075 none COC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 7, 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: [5, 4, 1, 4, 8, 8, 8, 19, 19, 19, 19, 19, 40, 40, 73, 108, 201, 201, 201, 201, 201, 19, 1, 1, 1, 1, 1, 5, 5, 5, 4, 8, 19, 19, 19, 19, 19, 73, 73, 201, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 42, 43, 44, 45, 46, 47, 48, 49, 50, 22, 23, 24, 25, 26] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 499
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498075 none COC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CCCC1 NO_LONG_NAME
dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 6, 7, 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: [10, 10, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 22, 108, 108, 108, 108, 108, 1, 10, 19, 19, 19, 19, 10, 10, 10, 10, 5, 1, 1, 1, 1, 1, 11, 12, 108, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 41] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49, 50])
total number of confs: 224
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498075 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498075
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498075/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498075
Building REAL300025498076
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498076'
/scratch/stefan/7787277/working/building/REAL300025498076 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498076

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498076/0 /scratch/stefan/7787277/working/building/REAL300025498076 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 966)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/966
`/scratch/stefan/7787277/working/3D/966' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NN(C)C(F)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498076.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498076.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498076/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498076 none CC1=NN(C)C(F)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens 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, 16, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 56, 144, 144, 144, 144, 144, 1, 16, 16, 16, 16, 16, 16, 6, 1, 1, 1, 1, 1, 28, 28, 144, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 10, 11, 12, 13, 14, 15, 16, 43, 26, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 298
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498076 none CC1=NN(C)C(F)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 198, 198, 198, 144, 144, 144, 144, 144, 111, 43, 111, 13, 1, 1, 1, 1, 1, 1, 1, 144, 201, 201, 201, 201, 201, 201, 198, 144, 144, 144, 144, 144, 43, 43, 1, 144, 144] 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, 42, 43])
total number of confs: 618
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498076 none CC1=NN(C)C(F)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total 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, 38, 38, 90, 127, 201, 201, 201, 201, 201, 16, 2, 2, 2, 2, 2, 2, 7, 16, 16, 16, 16, 16, 90, 90, 201, 16, 16] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 535
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498076 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498076
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498076/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498076
Building REAL300025498077
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498077'
/scratch/stefan/7787277/working/building/REAL300025498077 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498077

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498077/0 /scratch/stefan/7787277/working/building/REAL300025498077 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 967)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/967
`/scratch/stefan/7787277/working/3D/967' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(C(F)F)O2)C1)

`REAL300025498077.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498077.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498077/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498077 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(C(F)F)O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'O.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 12, 5, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 1, 5, 13, 24, 111, 111, 111, 111, 111, 1, 1, 1, 1, 1, 1, 4, 4, 4, 8, 8, 8, 8, 39, 39, 8, 1, 13, 13, 111, 1, 1, 1, 1, 1, 4, 8, 8, 39, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 10, 11, 12, 13, 14, 15, 39, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38])
total number of confs: 303
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498077 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(C(F)F)O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'O.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 12, 5, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 8, 24, 49, 79, 201, 201, 201, 201, 201, 8, 8, 8, 8, 5, 5, 1, 5, 1, 1, 1, 1, 1, 12, 12, 1, 8, 49, 49, 201, 8, 8, 8, 8, 8, 5, 1, 1, 12, 8, 8] 201
rigid atoms, others: [36, 37, 16, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40])
total number of confs: 457
number of broken/clashed sets: 50
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498077 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=C(C(F)F)O2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.3', 'F', 'F', 'O.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 5, 15, 15, 12, 5, 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, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [88, 42, 13, 1, 1, 1, 1, 1, 1, 1, 88, 111, 111, 111, 111, 111, 186, 186, 186, 201, 201, 201, 201, 201, 201, 201, 111, 42, 42, 1, 111, 111, 111, 111, 111, 186, 201, 201, 201, 111, 111] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 622
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498077 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498077
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498077/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498077
Building REAL300025498078
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498078'
/scratch/stefan/7787277/working/building/REAL300025498078 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498078

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498078/0 /scratch/stefan/7787277/working/building/REAL300025498078 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 968)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/968
`/scratch/stefan/7787277/working/3D/968' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)NC=N1)

`REAL300025498078.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498078.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498078/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498078 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.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, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [40, 23, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 11, 58, 58, 58, 58, 58, 1, 23, 23, 23, 40, 40, 40, 40, 40, 5, 1, 1, 1, 1, 1, 5, 5, 58, 1, 1, 23, 23] 201
rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 40, 22, 41] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43])
total number of confs: 192
number of broken/clashed sets: 99
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498078 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.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, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 200, 200, 89, 89, 89, 58, 58, 58, 58, 58, 45, 30, 45, 13, 1, 1, 1, 1, 1, 1, 1, 58, 200, 200, 200, 201, 201, 201, 201, 201, 89, 58, 58, 58, 58, 58, 30, 30, 1, 58, 58, 200, 200] 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: 458
number of broken/clashed sets: 99
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498078 none CCC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.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, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 1, 1, 1, 9, 9, 9, 23, 23, 23, 23, 23, 28, 28, 63, 103, 200, 200, 200, 200, 200, 23, 1, 1, 1, 6, 6, 6, 5, 5, 9, 23, 23, 23, 23, 23, 63, 63, 200, 23, 23, 1, 1] 201
rigid atoms, others: [1, 2, 3, 4, 42, 43, 23, 24, 25] set([0, 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: 484
number of broken/clashed sets: 99
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498078 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498078
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498078/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498078
Building REAL300025498079
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498079'
/scratch/stefan/7787277/working/building/REAL300025498079 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498079

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498079/0 /scratch/stefan/7787277/working/building/REAL300025498079 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 969)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/969
`/scratch/stefan/7787277/working/3D/969' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498079.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498079.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498079/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498079 none CN1C(=O)CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 43, 95, 95, 95, 95, 95, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 26, 26, 95, 1, 1] 140
rigid atoms, others: [38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45])
total number of confs: 234
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498079 none CN1C(=O)CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [140, 140, 140, 140, 140, 140, 140, 122, 122, 122, 95, 95, 95, 95, 95, 77, 40, 77, 13, 1, 1, 1, 1, 1, 1, 1, 95, 140, 140, 140, 140, 140, 140, 140, 140, 140, 140, 122, 95, 95, 95, 95, 95, 40, 40, 1, 95, 95] 140
rigid atoms, others: [45, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47])
total number of confs: 457
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498079 none CN1C(=O)CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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
140  conformations in input
total number of sets (complete confs): 140
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 32, 32, 70, 97, 140, 140, 140, 140, 140, 13, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 70, 70, 140, 13, 13] 140
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 34, 35, 32, 36, 33, 30, 31] set([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])
total number of confs: 393
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498079 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498079
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498079/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498079
Building REAL300025498080
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498080'
/scratch/stefan/7787277/working/building/REAL300025498080 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498080

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498080/0 /scratch/stefan/7787277/working/building/REAL300025498080 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 970)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/970
`/scratch/stefan/7787277/working/3D/970' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C=NC=C1CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498080.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498080.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498080/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498080 none CN1C=NC=C1CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens 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, 27, 26, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 56, 56, 56, 56, 56, 1, 37, 37, 37, 37, 37, 27, 27, 26, 26, 4, 1, 1, 1, 1, 1, 6, 6, 56, 1, 1] 201
rigid atoms, others: [45, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 46, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 191
number of broken/clashed sets: 73
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498080 none CN1C=NC=C1CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 166, 166, 82, 82, 82, 56, 56, 56, 56, 56, 44, 28, 44, 13, 1, 1, 1, 1, 1, 1, 1, 56, 201, 201, 201, 201, 201, 166, 166, 166, 166, 82, 56, 56, 56, 56, 56, 28, 28, 1, 56, 56] 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])
total number of confs: 724
number of broken/clashed sets: 73
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498080 none CN1C=NC=C1CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [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]
0  hydrogens need rotated
201  conformations in input
total 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, 5, 19, 19, 19, 37, 37, 37, 37, 37, 51, 51, 97, 137, 201, 201, 201, 201, 201, 37, 2, 2, 2, 1, 1, 4, 4, 5, 5, 19, 37, 37, 37, 37, 37, 97, 97, 201, 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: 576
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498080 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498080
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498080/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498080
Building REAL300025498081
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498081'
/scratch/stefan/7787277/working/building/REAL300025498081 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498081

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498081/0 /scratch/stefan/7787277/working/building/REAL300025498081 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 971)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/971
`/scratch/stefan/7787277/working/3D/971' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NNC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498081.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498081.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498081/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498081 none CC1=NNC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 46, 151, 151, 151, 151, 151, 1, 11, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 20, 20, 151, 1, 1] 201
rigid atoms, others: [34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 43, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41])
total number of confs: 270
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498081 none CC1=NNC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 191, 191, 191, 151, 151, 151, 151, 151, 128, 62, 128, 13, 1, 1, 1, 1, 1, 1, 1, 151, 201, 201, 201, 201, 201, 201, 201, 191, 151, 151, 151, 151, 151, 62, 62, 1, 151, 151] 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])
total number of confs: 617
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498081 none CC1=NNC(C)=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 8, 1, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 17, 17, 17, 17, 17, 35, 35, 70, 118, 201, 201, 201, 201, 201, 17, 2, 2, 2, 1, 2, 2, 2, 10, 17, 17, 17, 17, 17, 70, 70, 201, 17, 17] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 479
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498081 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498081
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498081/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498081
Building REAL300025498082
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498082'
/scratch/stefan/7787277/working/building/REAL300025498082 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498082

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498082/0 /scratch/stefan/7787277/working/building/REAL300025498082 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 972)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/972
`/scratch/stefan/7787277/working/3D/972' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3C=CC=CN3N=C2)C1)

`REAL300025498082.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498082.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498082/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498082 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3C=CC=CN3N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 5, 7, 7, 6, 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, 19, 33, 93, 93, 93, 93, 93, 1, 1, 1, 1, 1, 1, 5, 5, 5, 24, 24, 24, 24, 24, 24, 24, 24, 1, 19, 19, 93, 1, 1, 1, 1, 1, 5, 24, 24, 24, 24, 24, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 210
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498082 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3C=CC=CN3N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 5, 7, 7, 6, 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: [59, 24, 59, 100, 141, 201, 201, 201, 201, 201, 24, 24, 24, 24, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 100, 100, 201, 24, 24, 24, 24, 24, 8, 1, 1, 1, 1, 1, 24, 24] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 560
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498082 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3C=CC=CN3N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.2', 'C.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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 8, 1, 5, 7, 7, 6, 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: [74, 39, 13, 1, 1, 1, 1, 1, 1, 1, 74, 93, 93, 93, 93, 93, 128, 128, 128, 201, 201, 201, 201, 201, 201, 201, 201, 93, 39, 39, 1, 93, 93, 93, 93, 93, 128, 201, 201, 201, 201, 201, 93, 93] 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: 530
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498082 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498082
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498082/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498082
Building REAL300025498083
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498083'
/scratch/stefan/7787277/working/building/REAL300025498083 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498083

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498083/0 /scratch/stefan/7787277/working/building/REAL300025498083 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 973)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/973
`/scratch/stefan/7787277/working/3D/973' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)=N1)

`REAL300025498083.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498083.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498083/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498083 none CC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 25, 25, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 32, 70, 70, 70, 70, 70, 1, 25, 25, 25, 25, 25, 25, 25, 5, 1, 1, 1, 1, 1, 18, 18, 70, 1, 1, 25, 25, 25] 201
rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 40, 41, 23] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44])
total number of confs: 284
number of broken/clashed sets: 16
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498083 none CC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [96, 96, 201, 201, 96, 96, 96, 70, 70, 70, 70, 70, 60, 39, 60, 13, 1, 1, 1, 1, 1, 1, 1, 70, 201, 201, 201, 201, 201, 201, 201, 96, 70, 70, 70, 70, 70, 39, 39, 1, 70, 70, 201, 201, 201] 201
rigid atoms, others: [39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44])
total number of confs: 1189
number of broken/clashed sets: 16
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498083 none CC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(C)=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 9, 9, 9, 25, 25, 25, 25, 25, 51, 51, 93, 136, 201, 201, 201, 201, 201, 25, 1, 1, 1, 2, 2, 2, 1, 9, 25, 25, 25, 25, 25, 93, 93, 201, 25, 25, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 26, 30] set([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])
total number of confs: 566
number of broken/clashed sets: 16
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498083 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498083
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498083/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498083
Building REAL300025498084
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498084'
/scratch/stefan/7787277/working/building/REAL300025498084 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498084

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498084/0 /scratch/stefan/7787277/working/building/REAL300025498084 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 974)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/974
`/scratch/stefan/7787277/working/3D/974' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498084.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498084.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498084/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498084 none CC1=NC=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 23, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 32, 73, 73, 73, 73, 73, 1, 23, 23, 23, 23, 23, 23, 5, 1, 1, 1, 1, 1, 18, 18, 73, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 41, 25, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 191
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498084 none CC1=NC=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 73, 73, 73, 73, 73, 60, 38, 60, 13, 1, 1, 1, 1, 1, 1, 1, 73, 201, 201, 201, 201, 201, 201, 101, 73, 73, 73, 73, 73, 38, 38, 1, 73, 73] 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])
total number of confs: 497
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498084 none CC1=NC=CC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 23, 23, 23, 23, 23, 52, 52, 89, 130, 201, 201, 201, 201, 201, 23, 2, 2, 2, 1, 1, 1, 9, 23, 23, 23, 23, 23, 89, 89, 201, 23, 23] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 29, 30, 31] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 545
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498084 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498084
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498084/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498084
Building REAL300025498085
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498085'
/scratch/stefan/7787277/working/building/REAL300025498085 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498085

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498085/0 /scratch/stefan/7787277/working/building/REAL300025498085 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 975)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/975
`/scratch/stefan/7787277/working/3D/975' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)CCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498085.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498085.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498085/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498085 none CC(C)CCCCC(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 168, 201, 201, 168, 179, 61, 61, 61, 35, 35, 35, 35, 35, 32, 23, 32, 12, 1, 1, 1, 1, 1, 1, 1, 35, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 179, 61, 35, 35, 35, 35, 35, 23, 23, 1, 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])
total number of confs: 1229
number of broken/clashed sets: 51
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498085 none CC(C)CCCCC(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [40, 34, 40, 40, 34, 27, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 35, 35, 35, 35, 35, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 27, 27, 5, 1, 1, 1, 1, 1, 5, 5, 35, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49])
total number of confs: 293
number of broken/clashed sets: 51
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498085 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498085
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498085/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498085
Building REAL300025498086
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498086'
/scratch/stefan/7787277/working/building/REAL300025498086 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498086

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498086/0 /scratch/stefan/7787277/working/building/REAL300025498086 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 976)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/976
`/scratch/stefan/7787277/working/3D/976' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC[NH+](CC)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498086.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498086.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498086/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498086 none CC[NH+](CC)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 9, 6, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [33, 33, 31, 33, 33, 33, 23, 23, 23, 19, 19, 19, 19, 19, 17, 15, 17, 10, 1, 1, 1, 1, 1, 1, 1, 19, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 31, 31, 23, 19, 19, 19, 19, 19, 15, 15, 1, 19, 19] 33
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: 124
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498086 none CC[NH+](CC)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 9, 6, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
33  conformations in input
total number of sets (complete confs): 33
using default count positions algorithm for smaller data
unique positions, atoms: [12, 12, 9, 12, 12, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 8, 19, 19, 19, 19, 19, 1, 12, 12, 12, 12, 12, 13, 13, 13, 13, 13, 9, 9, 4, 1, 1, 1, 1, 1, 7, 7, 19, 1, 1] 33
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 90
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498086 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498086
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498086/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498086
Building REAL300025498087
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498087'
/scratch/stefan/7787277/working/building/REAL300025498087 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498087

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498087/0 /scratch/stefan/7787277/working/building/REAL300025498087 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 977)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/977
`/scratch/stefan/7787277/working/3D/977' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498087.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498087.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498087/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498087 none CCC(F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 201, 181, 201, 181, 181, 116, 116, 116, 116, 116, 88, 53, 88, 13, 1, 1, 1, 1, 1, 1, 1, 116, 201, 201, 201, 201, 201, 201, 181, 116, 116, 116, 116, 116, 53, 53, 1, 116, 116] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 703
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: REAL300025498087 none CCC(F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 15, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [27, 19, 5, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 25, 116, 116, 116, 116, 116, 1, 29, 29, 29, 29, 29, 19, 5, 1, 1, 1, 1, 1, 11, 11, 116, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 6, 7, 8, 9, 10, 11, 12, 22, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 306
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498087 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498087
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498087/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498087
Building REAL300025498088
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498088'
/scratch/stefan/7787277/working/building/REAL300025498088 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498088

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498088/0 /scratch/stefan/7787277/working/building/REAL300025498088 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 978)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/978
`/scratch/stefan/7787277/working/3D/978' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCF)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498088.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498088.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498088/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498088 none O=C(CCCF)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 179, 199, 201, 47, 47, 47, 47, 47, 37, 28, 37, 13, 1, 1, 1, 1, 1, 1, 1, 47, 179, 179, 201, 201, 201, 201, 73, 47, 47, 47, 47, 47, 28, 28, 1, 47, 47] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 826
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: REAL300025498088 none O=C(CCCF)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'F', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 15, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 23, 27, 42, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 14, 47, 47, 47, 47, 47, 1, 23, 23, 36, 36, 40, 38, 5, 1, 1, 1, 1, 1, 10, 10, 47, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 6, 7, 8, 9, 10, 11, 12, 22, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 310
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498088 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498088
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498088/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498088
Building REAL300025498089
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498089'
/scratch/stefan/7787277/working/building/REAL300025498089 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498089

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498089/0 /scratch/stefan/7787277/working/building/REAL300025498089 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 979)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/979
`/scratch/stefan/7787277/working/3D/979' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(F)(F)F)

`REAL300025498089.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498089.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498089/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498089 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', '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', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 92, 92, 92, 92, 92, 82, 49, 82, 13, 1, 1, 1, 1, 1, 1, 1, 92, 201, 201, 201, 201, 201, 201, 201, 201, 130, 92, 92, 92, 92, 92, 49, 49, 1, 92, 92] 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])
total number of confs: 781
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: REAL300025498089 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C(F)(F)F NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', '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', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 15, 15, 15, 7, 7, 7, 7, 6, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 5, 5, 14, 29, 92, 92, 92, 92, 92, 1, 19, 19, 19, 19, 19, 19, 19, 19, 4, 1, 1, 1, 1, 1, 14, 14, 92, 1, 1] 201
rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 39, 20, 38, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 216
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498089 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498089
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498089/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498089
Building REAL300025498090
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498090'
/scratch/stefan/7787277/working/building/REAL300025498090 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498090

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498090/0 /scratch/stefan/7787277/working/building/REAL300025498090 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 980)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/980
`/scratch/stefan/7787277/working/3D/980' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=COC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498090.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498090.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498090/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498090 none CC1=COC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 32, 124, 124, 124, 124, 124, 1, 17, 17, 17, 17, 17, 5, 1, 1, 1, 1, 1, 13, 13, 124, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 220
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498090 none CC1=COC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 166, 166, 166, 124, 124, 124, 124, 124, 103, 47, 103, 13, 1, 1, 1, 1, 1, 1, 1, 124, 201, 201, 201, 201, 201, 166, 124, 124, 124, 124, 124, 47, 47, 1, 124, 124] 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])
total number of confs: 576
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498090 none CC1=COC=C1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 12, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 17, 17, 17, 17, 17, 34, 34, 66, 106, 201, 201, 201, 201, 201, 17, 2, 2, 2, 1, 1, 7, 17, 17, 17, 17, 17, 66, 66, 201, 17, 17] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 489
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498090 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498090
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498090/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498090
Building REAL300025498091
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498091'
/scratch/stefan/7787277/working/building/REAL300025498091 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498091

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498091/0 /scratch/stefan/7787277/working/building/REAL300025498091 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 981)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/981
`/scratch/stefan/7787277/working/3D/981' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C[C@H]1C[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498091.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498091.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498091/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498091 none C[C@H]1C[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 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, 6, 7, 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: [20, 20, 20, 20, 4, 20, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 13, 26, 89, 89, 89, 89, 89, 1, 20, 20, 20, 20, 20, 4, 1, 1, 1, 1, 1, 13, 13, 89, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 194
number of broken/clashed sets: 12
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498091 none C[C@H]1C[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 112, 201, 112, 112, 89, 89, 89, 89, 89, 80, 35, 80, 13, 1, 1, 1, 1, 1, 1, 1, 89, 201, 201, 201, 201, 201, 112, 89, 89, 89, 89, 89, 35, 35, 1, 89, 89] 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])
total number of confs: 667
number of broken/clashed sets: 12
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498091 none C[C@H]1C[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 20, 20, 20, 20, 20, 42, 42, 80, 109, 201, 201, 201, 201, 201, 20, 2, 2, 2, 1, 1, 11, 20, 20, 20, 20, 20, 80, 80, 201, 20, 20] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 509
number of broken/clashed sets: 12
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498091 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498091
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498091/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498091
Building REAL300025498092
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498092'
/scratch/stefan/7787277/working/building/REAL300025498092 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498092

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498092/0 /scratch/stefan/7787277/working/building/REAL300025498092 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 982)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/982
`/scratch/stefan/7787277/working/3D/982' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CCC1)

`REAL300025498092.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498092.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498092/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498092 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 5, 5, 7, 7, 7, 6, 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]
0  hydrogens 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, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 29, 89, 89, 89, 89, 89, 1, 15, 15, 15, 15, 15, 15, 15, 5, 1, 1, 1, 1, 1, 14, 14, 89, 1, 1, 15, 15, 15, 15, 15, 15] 201
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 37, 20, 38, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40, 41, 42, 43, 44])
total number of confs: 198
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498092 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 5, 5, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 109, 109, 109, 89, 89, 89, 89, 89, 71, 43, 71, 12, 1, 1, 1, 1, 1, 1, 1, 89, 201, 201, 201, 201, 201, 201, 201, 109, 89, 89, 89, 89, 89, 43, 43, 1, 89, 89, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [36, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 640
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498092 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C=CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 5, 5, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  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, 15, 15, 15, 15, 15, 41, 41, 70, 113, 201, 201, 201, 201, 201, 15, 1, 1, 1, 1, 2, 2, 2, 6, 15, 15, 15, 15, 15, 70, 70, 201, 15, 15, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 39, 40, 41, 42, 43, 44, 21, 22, 23, 24] set([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])
total number of confs: 502
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498092 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498092
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498092/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498092
Building REAL300025498093
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498093'
/scratch/stefan/7787277/working/building/REAL300025498093 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498093

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498093/0 /scratch/stefan/7787277/working/building/REAL300025498093 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 983)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/983
`/scratch/stefan/7787277/working/3D/983' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)CC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498093.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498093.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498093/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498093 none CN1C(=O)CC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 5, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 40, 136, 136, 136, 136, 136, 1, 12, 12, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 19, 19, 136, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 44, 10, 11, 12, 13, 14, 15, 16, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 263
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498093 none CN1C(=O)CC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 175, 201, 175, 175, 136, 135, 135, 136, 135, 103, 45, 103, 12, 1, 1, 1, 1, 1, 1, 1, 135, 201, 201, 201, 201, 201, 201, 201, 175, 136, 136, 136, 136, 136, 45, 45, 1, 135, 135] 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, 43, 44])
total number of confs: 642
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498093 none CN1C(=O)CC[C@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 12, 12, 12, 12, 12, 30, 30, 67, 108, 201, 201, 201, 201, 201, 12, 2, 2, 2, 1, 1, 1, 1, 5, 12, 12, 12, 12, 12, 67, 67, 201, 12, 12] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 33, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 489
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498093 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498093
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498093/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498093
Building REAL300025498094
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498094'
/scratch/stefan/7787277/working/building/REAL300025498094 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498094

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498094/0 /scratch/stefan/7787277/working/building/REAL300025498094 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 984)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/984
`/scratch/stefan/7787277/working/3D/984' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1N=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=N1)

`REAL300025498094.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498094.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498094/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498094 none CN1N=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 6, 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, 6, 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: [12, 12, 12, 12, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 26, 44, 122, 122, 122, 122, 122, 1, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 26, 26, 122, 1, 1] 201
rigid atoms, others: [32, 33, 37, 38, 7, 8, 9, 10, 11, 12, 13, 23, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 34, 35, 36])
total number of confs: 256
number of broken/clashed sets: 21
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498094 none CN1N=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 154, 154, 154, 122, 122, 122, 122, 122, 91, 42, 91, 13, 1, 1, 1, 1, 1, 1, 1, 122, 201, 201, 201, 201, 154, 122, 122, 122, 122, 122, 42, 42, 1, 122, 122] 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])
total number of confs: 569
number of broken/clashed sets: 21
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498094 none CN1N=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', '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.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 8, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 12, 12, 12, 37, 37, 86, 119, 201, 201, 201, 201, 201, 12, 1, 2, 2, 2, 4, 12, 12, 12, 12, 12, 86, 86, 201, 12, 12] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 527
number of broken/clashed sets: 21
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498094 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498094
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498094/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498094
Building REAL300025498095
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498095'
/scratch/stefan/7787277/working/building/REAL300025498095 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498095

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498095/0 /scratch/stefan/7787277/working/building/REAL300025498095 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 985)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/985
`/scratch/stefan/7787277/working/3D/985' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498095.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498095.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498095/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498095 none CC1(C)CCCC1C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 7, 7, 22, 61, 169, 169, 169, 169, 169, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 22, 22, 169, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 299
number of broken/clashed sets: 17
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498095 none CC1(C)CCCC1C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 169, 169, 169, 169, 169, 142, 58, 142, 13, 1, 1, 1, 1, 1, 1, 1, 169, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 169, 169, 169, 169, 169, 58, 58, 1, 169, 169] 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: 612
number of broken/clashed sets: 17
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498095 none CC1(C)CCCC1C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 5, 22, 22, 52, 109, 201, 201, 201, 201, 201, 5, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 5, 5, 5, 5, 5, 52, 52, 201, 5, 5] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 7, 34, 35, 36, 38, 37, 5] 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, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49])
total number of confs: 437
number of broken/clashed sets: 17
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498095 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498095
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498095/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498095
Building REAL300025498096
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498096'
/scratch/stefan/7787277/working/building/REAL300025498096 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498096

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498096/0 /scratch/stefan/7787277/working/building/REAL300025498096 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 986)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/986
`/scratch/stefan/7787277/working/3D/986' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025498096.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498096.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498096/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498096 none CC1CCC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 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, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [62, 62, 62, 62, 29, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 12, 43, 43, 43, 43, 43, 1, 62, 62, 62, 62, 62, 62, 62, 62, 62, 62, 29, 29, 4, 1, 1, 1, 1, 1, 7, 7, 43, 1, 1, 62, 62] 201
rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 40, 46, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 48, 49])
total number of confs: 280
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498096 none CC1CCC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 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, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 186, 80, 80, 80, 43, 43, 43, 43, 43, 35, 25, 35, 13, 1, 1, 1, 1, 1, 1, 1, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 186, 186, 80, 43, 43, 43, 43, 43, 25, 25, 1, 43, 43, 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: 775
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498096 none CC1CCC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 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, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
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, 28, 28, 28, 62, 62, 62, 62, 62, 69, 69, 81, 124, 201, 201, 201, 201, 201, 62, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 28, 62, 62, 62, 62, 62, 81, 81, 201, 62, 62, 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: 496
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498096 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498096
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498096/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498096
Building REAL300025498097
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498097'
/scratch/stefan/7787277/working/building/REAL300025498097 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498097

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498097/0 /scratch/stefan/7787277/working/building/REAL300025498097 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 987)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/987
`/scratch/stefan/7787277/working/3D/987' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N(C)N=C1)

`REAL300025498097.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498097.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498097/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498097 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 8, 1, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [19, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 28, 103, 103, 103, 103, 103, 1, 19, 19, 19, 19, 19, 19, 19, 4, 1, 1, 1, 1, 1, 14, 14, 103, 1, 1, 19, 19, 19, 19] 201
rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 21, 39, 38, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42, 43])
total number of confs: 193
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498097 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 8, 1, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 148, 148, 148, 103, 103, 103, 103, 103, 85, 48, 85, 13, 1, 1, 1, 1, 1, 1, 1, 103, 201, 201, 201, 201, 201, 201, 201, 148, 103, 103, 103, 103, 103, 48, 48, 1, 103, 103, 201, 201, 201, 201] 201
rigid atoms, others: [37, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43])
total number of confs: 569
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498097 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 8, 1, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 11, 11, 11, 19, 19, 19, 19, 19, 34, 34, 69, 114, 201, 201, 201, 201, 201, 19, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 19, 19, 19, 69, 69, 201, 19, 19, 2, 2, 2, 1] 201
rigid atoms, others: [0, 1, 2, 3, 43, 22, 23, 24, 25] set([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: 484
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498097 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498097
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498097/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498097
Building REAL300025498098
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498098'
/scratch/stefan/7787277/working/building/REAL300025498098 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498098

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498098/0 /scratch/stefan/7787277/working/building/REAL300025498098 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 988)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/988
`/scratch/stefan/7787277/working/3D/988' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C(F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498098.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498098.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498098/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498098 none CC(C)C(F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 186, 201, 141, 186, 141, 141, 95, 95, 95, 95, 95, 76, 50, 76, 13, 1, 1, 1, 1, 1, 1, 1, 95, 201, 201, 201, 201, 201, 201, 201, 186, 141, 95, 95, 95, 95, 95, 50, 50, 1, 95, 95] 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])
total number of confs: 778
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: REAL300025498098 none CC(C)C(F)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 15, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 19, 33, 5, 19, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 12, 21, 95, 95, 95, 95, 95, 1, 33, 33, 33, 33, 33, 33, 33, 19, 5, 1, 1, 1, 1, 1, 12, 12, 95, 1, 1] 201
rigid atoms, others: [33, 34, 35, 36, 37, 7, 8, 9, 10, 11, 12, 13, 41, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 38, 39, 40])
total number of confs: 293
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498098 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498098
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498098/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498098
Building REAL300025498099
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498099'
/scratch/stefan/7787277/working/building/REAL300025498099 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498099

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498099/0 /scratch/stefan/7787277/working/building/REAL300025498099 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 989)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/989
`/scratch/stefan/7787277/working/3D/989' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1)

`REAL300025498099.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498099.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498099/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498099 none CCCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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: [18, 18, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 26, 75, 75, 75, 75, 75, 1, 14, 14, 14, 18, 18, 18, 18, 18, 18, 18, 4, 1, 1, 1, 1, 1, 13, 13, 75, 1, 1, 14, 14, 14, 14, 14, 14] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47, 48, 49])
total number of confs: 191
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498099 none CCCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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: [201, 201, 201, 128, 128, 128, 75, 75, 75, 75, 75, 60, 27, 60, 13, 1, 1, 1, 1, 1, 1, 1, 75, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 128, 75, 75, 75, 75, 75, 27, 27, 1, 75, 75, 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])
total number of confs: 635
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498099 none CCCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 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: [5, 5, 1, 1, 1, 6, 6, 6, 14, 14, 14, 14, 14, 33, 33, 67, 115, 201, 201, 201, 201, 201, 14, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 6, 14, 14, 14, 14, 14, 67, 67, 201, 14, 14, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [2, 3, 4, 44, 45, 46, 47, 48, 49, 23, 24, 25] set([0, 1, 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: 496
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498099 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498099
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498099/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498099
Building REAL300025498100
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498100'
/scratch/stefan/7787277/working/building/REAL300025498100 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498100

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498100/0 /scratch/stefan/7787277/working/building/REAL300025498100 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 990)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/990
`/scratch/stefan/7787277/working/3D/990' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(C)C(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498100.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498100.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498100/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498100 none C=CC(C)C(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 200, 201, 143, 200, 143, 143, 99, 99, 99, 99, 99, 78, 30, 77, 13, 1, 1, 1, 1, 1, 1, 1, 99, 201, 201, 201, 201, 201, 201, 201, 200, 200, 200, 200, 143, 99, 99, 99, 99, 99, 30, 30, 1, 99, 99] 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])
total number of confs: 761
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: REAL300025498100 none C=CC(C)C(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [30, 21, 18, 21, 4, 18, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 26, 99, 99, 99, 99, 99, 1, 30, 30, 30, 21, 21, 21, 21, 18, 18, 18, 18, 4, 1, 1, 1, 1, 1, 13, 13, 99, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 270
number of broken/clashed sets: 20
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498100 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498100
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498100/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498100
Building REAL300025498101
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498101'
/scratch/stefan/7787277/working/building/REAL300025498101 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498101

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498101/0 /scratch/stefan/7787277/working/building/REAL300025498101 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 991)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/991
`/scratch/stefan/7787277/working/3D/991' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1)

`REAL300025498101.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498101.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498101/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498101 none CCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [14, 14, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 29, 72, 72, 72, 72, 72, 1, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 1, 1, 1, 1, 14, 14, 72, 1, 1, 14, 14, 14, 14, 14, 14] 201
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 40, 21, 39, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46])
total number of confs: 169
number of broken/clashed sets: 5
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498101 none CCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 102, 102, 102, 72, 72, 72, 72, 72, 62, 34, 62, 13, 1, 1, 1, 1, 1, 1, 1, 72, 201, 201, 201, 201, 201, 201, 201, 201, 102, 72, 72, 72, 72, 72, 34, 34, 1, 72, 72, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [38, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 625
number of broken/clashed sets: 5
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498101 none CCC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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]
0  hydrogens need 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, 14, 14, 14, 14, 14, 32, 32, 63, 103, 201, 201, 201, 201, 201, 14, 1, 1, 1, 3, 3, 3, 3, 3, 6, 14, 14, 14, 14, 14, 63, 63, 201, 14, 14, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [1, 2, 3, 41, 42, 43, 44, 45, 46, 22, 23, 24] set([0, 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: 459
number of broken/clashed sets: 5
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498101 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498101
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498101/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498101
Building REAL300025498102
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498102'
/scratch/stefan/7787277/working/building/REAL300025498102 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498102

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498102/0 /scratch/stefan/7787277/working/building/REAL300025498102 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 992)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/992
`/scratch/stefan/7787277/working/3D/992' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3(CCC3)C2)C1)

`REAL300025498102.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498102.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498102/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498102 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3(CCC3)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 18, 31, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 5, 5, 5, 24, 24, 24, 24, 24, 24, 1, 18, 18, 68, 1, 1, 1, 1, 1, 5, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1] 201
rigid atoms, others: [32, 1, 33, 10, 11, 12, 13, 14, 15, 46, 25, 47, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 205
number of broken/clashed sets: 18
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498102 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3(CCC3)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 24, 53, 93, 134, 201, 201, 201, 201, 201, 24, 24, 24, 24, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 24, 93, 93, 201, 24, 24, 24, 24, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 201
rigid atoms, others: [35, 36, 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, 46, 47])
total number of confs: 552
number of broken/clashed sets: 18
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498102 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2CC3(CCC3)C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 38, 13, 1, 1, 1, 1, 1, 1, 1, 58, 68, 68, 68, 68, 68, 83, 83, 83, 201, 201, 201, 201, 201, 201, 68, 38, 38, 1, 68, 68, 68, 68, 68, 83, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 68, 68] 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: 638
number of broken/clashed sets: 18
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498102 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498102
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498102/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498102
Building REAL300025498103
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498103'
/scratch/stefan/7787277/working/building/REAL300025498103 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498103

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498103/0 /scratch/stefan/7787277/working/building/REAL300025498103 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 993)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/993
`/scratch/stefan/7787277/working/3D/993' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC#CCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498103.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498103.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498103/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498103 none CC#CCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 143, 130, 42, 42, 42, 29, 29, 29, 29, 29, 28, 22, 28, 12, 1, 1, 1, 1, 1, 1, 1, 29, 201, 201, 201, 187, 186, 176, 176, 130, 130, 42, 29, 29, 29, 29, 29, 22, 22, 1, 29, 29] 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])
total number of confs: 1026
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: REAL300025498103 none CC#CCCCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 1, 1, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [48, 48, 48, 23, 19, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 8, 29, 29, 29, 29, 29, 1, 48, 48, 48, 45, 44, 30, 30, 19, 19, 5, 1, 1, 1, 1, 1, 5, 5, 29, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 283
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498103 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498103
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498103/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498103
Building REAL300025498104
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498104'
/scratch/stefan/7787277/working/building/REAL300025498104 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498104

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498104/0 /scratch/stefan/7787277/working/building/REAL300025498104 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 994)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/994
`/scratch/stefan/7787277/working/3D/994' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1)

`REAL300025498104.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498104.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498104/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498104 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [5, 1, 5, 12, 20, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 23, 23, 23, 23, 23, 23, 23, 1, 12, 12, 75, 1, 1, 1, 1, 1, 5, 23, 23, 23, 23, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 41, 10, 11, 12, 13, 14, 15, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40])
total number of confs: 182
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498104 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [45, 23, 45, 82, 112, 201, 201, 201, 201, 201, 23, 23, 23, 23, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 82, 82, 201, 23, 23, 23, 23, 23, 10, 1, 1, 1, 1, 23, 23] 201
rigid atoms, others: [37, 38, 39, 40, 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, 41, 42])
total number of confs: 530
number of broken/clashed sets: 25
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498104 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2[C@@H]3COC[C@@H]32)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 7, 5, 12, 5, 5, 7, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [58, 37, 12, 1, 1, 1, 1, 1, 1, 1, 58, 75, 75, 75, 75, 75, 108, 108, 108, 201, 201, 201, 201, 201, 201, 201, 201, 75, 37, 37, 1, 75, 75, 75, 75, 75, 108, 201, 201, 201, 201, 75, 75] 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: 642
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498104 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498104
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498104/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498104
Building REAL300025498105
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498105'
/scratch/stefan/7787277/working/building/REAL300025498105 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498105

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498105/0 /scratch/stefan/7787277/working/building/REAL300025498105 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 995)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/995
`/scratch/stefan/7787277/working/3D/995' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCCC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498105.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498105.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498105/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498105 none O=C(CCCC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need 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, 15, 20, 22, 39, 39, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 46, 46, 46, 46, 46, 1, 15, 15, 22, 22, 22, 22, 39, 39, 39, 39, 39, 3, 1, 1, 1, 1, 1, 5, 5, 46, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 237
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498105 none O=C(CCCC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 164, 168, 179, 201, 201, 46, 46, 46, 46, 46, 43, 30, 43, 13, 1, 1, 1, 1, 1, 1, 1, 46, 164, 164, 179, 179, 179, 179, 201, 201, 201, 201, 201, 48, 46, 46, 46, 46, 46, 30, 30, 1, 46, 46] 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])
total number of confs: 864
number of broken/clashed sets: 63
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498105 none O=C(CCCC1CC1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 5, 5, 5, 5, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens 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, 3, 3, 1, 1, 1, 1, 30, 30, 39, 39, 39, 39, 39, 41, 41, 84, 138, 201, 201, 201, 201, 201, 39, 7, 7, 3, 3, 3, 3, 1, 1, 1, 1, 1, 30, 39, 39, 39, 39, 39, 84, 84, 201, 39, 39] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 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, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 561
number of broken/clashed sets: 63
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498105 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498105
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498105/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498105
Building REAL300025498106
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498106'
/scratch/stefan/7787277/working/building/REAL300025498106 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498106

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498106/0 /scratch/stefan/7787277/working/building/REAL300025498106 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 996)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/996
`/scratch/stefan/7787277/working/3D/996' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1=O)

`REAL300025498106.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498106.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498106/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498106 none CN1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [25, 25, 25, 25, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 45, 119, 119, 119, 119, 119, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 4, 1, 1, 1, 1, 1, 25, 25, 119, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 278
number of broken/clashed sets: 8
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498106 none CN1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 201, 154, 154, 154, 119, 119, 119, 119, 119, 90, 39, 90, 13, 1, 1, 1, 1, 1, 1, 1, 119, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 154, 119, 119, 119, 119, 119, 39, 39, 1, 119, 119] 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])
total number of confs: 629
number of broken/clashed sets: 8
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498106 none CN1CCC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 1, 10, 10, 10, 25, 25, 25, 25, 25, 53, 53, 110, 141, 201, 201, 201, 201, 201, 25, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 10, 25, 25, 25, 25, 25, 110, 110, 201, 25, 25] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 24, 25, 33, 29, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 581
number of broken/clashed sets: 8
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498106 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498106
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498106/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498106
Building REAL300025498107
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498107'
/scratch/stefan/7787277/working/building/REAL300025498107 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498107

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498107/0 /scratch/stefan/7787277/working/building/REAL300025498107 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 997)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/997
`/scratch/stefan/7787277/working/3D/997' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(OCC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498107.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498107.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498107/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498107 none CCCC(OCC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 190, 156, 117, 156, 156, 156, 117, 117, 76, 76, 76, 76, 76, 54, 36, 54, 13, 1, 1, 1, 1, 1, 1, 1, 76, 201, 201, 201, 201, 201, 201, 201, 156, 156, 156, 156, 156, 156, 117, 76, 76, 76, 76, 76, 36, 36, 1, 76, 76] 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: 889
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: REAL300025498107 none CCCC(OCC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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, 5, 12, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 24, 11, 5, 11, 12, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 14, 76, 76, 76, 76, 76, 1, 26, 26, 26, 26, 26, 26, 26, 11, 12, 12, 12, 12, 12, 5, 1, 1, 1, 1, 1, 8, 8, 76, 1, 1] 201
rigid atoms, others: [43, 40, 9, 10, 11, 12, 13, 14, 44, 48, 49, 41, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45, 46, 47])
total number of confs: 230
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498107 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498107
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498107/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498107
Building REAL300025498108
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498108'
/scratch/stefan/7787277/working/building/REAL300025498108 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498108

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498108/0 /scratch/stefan/7787277/working/building/REAL300025498108 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 998)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/998
`/scratch/stefan/7787277/working/3D/998' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498108.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498108.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498108/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498108 none CC1(C)CCC1C(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [11, 11, 11, 11, 11, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 36, 113, 113, 113, 113, 113, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 16, 16, 113, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 222
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498108 none CC1(C)CCC1C(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 158, 158, 158, 113, 113, 113, 113, 113, 91, 44, 91, 13, 1, 1, 1, 1, 1, 1, 1, 113, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 158, 113, 113, 113, 113, 113, 44, 44, 1, 113, 113] 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])
total number of confs: 668
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498108 none CC1(C)CCC1C(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 11, 11, 11, 11, 11, 29, 29, 63, 110, 201, 201, 201, 201, 201, 11, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 63, 63, 201, 11, 11] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 34, 35, 33, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 473
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498108 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498108
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498108/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498108
Building REAL300025498109
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498109'
/scratch/stefan/7787277/working/building/REAL300025498109 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498109

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498109/0 /scratch/stefan/7787277/working/building/REAL300025498109 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 999)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/999
`/scratch/stefan/7787277/working/3D/999' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=COC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025498109.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498109.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498109/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498109 none CC1=COC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 33, 57, 155, 155, 155, 155, 155, 1, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 33, 33, 155, 1, 1, 13] 201
rigid atoms, others: [32, 33, 34, 38, 7, 8, 9, 10, 11, 12, 13, 23, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40])
total number of confs: 317
number of broken/clashed sets: 27
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498109 none CC1=COC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations 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, 155, 155, 155, 155, 155, 114, 47, 114, 13, 1, 1, 1, 1, 1, 1, 1, 155, 201, 201, 201, 201, 201, 199, 155, 155, 155, 155, 155, 47, 47, 1, 155, 155, 201] 201
rigid atoms, others: [37, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40])
total number of confs: 605
number of broken/clashed sets: 27
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498109 none CC1=COC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 12, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 94, 129, 201, 201, 201, 201, 201, 13, 1, 2, 2, 2, 1, 4, 13, 13, 13, 13, 13, 94, 94, 201, 13, 13, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 24, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 545
number of broken/clashed sets: 27
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498109 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498109
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498109/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498109
Building REAL300025498110
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498110'
/scratch/stefan/7787277/working/building/REAL300025498110 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498110

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498110/0 /scratch/stefan/7787277/working/building/REAL300025498110 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1000)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1000
`/scratch/stefan/7787277/working/3D/1000' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC(=O)N2)C1)

`REAL300025498110.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498110.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498110/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498110 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 14, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock 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]
0  hydrogens need 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, 21, 81, 81, 81, 81, 81, 1, 1, 1, 1, 1, 1, 4, 4, 4, 28, 28, 28, 28, 28, 1, 10, 10, 81, 1, 1, 1, 1, 1, 4, 28, 28, 1, 1] 201
rigid atoms, others: [32, 1, 36, 37, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35])
total number of confs: 163
number of broken/clashed sets: 9
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498110 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 14, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 28, 46, 86, 125, 201, 201, 201, 201, 201, 28, 28, 28, 28, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 28, 86, 86, 201, 28, 28, 28, 28, 28, 12, 1, 1, 28, 28] 201
rigid atoms, others: [34, 35, 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, 36, 37])
total number of confs: 543
number of broken/clashed sets: 9
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498110 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CSC(=O)N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 14, 1, 11, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7]
dock 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]
0  hydrogens 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, 42, 13, 1, 1, 1, 1, 1, 1, 1, 64, 81, 81, 81, 81, 81, 113, 113, 113, 201, 201, 201, 201, 201, 81, 42, 42, 1, 81, 81, 81, 81, 81, 113, 201, 201, 81, 81] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37])
total number of confs: 510
number of broken/clashed sets: 9
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498110 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498110
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498110/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498110
Building REAL300025498111
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498111'
/scratch/stefan/7787277/working/building/REAL300025498111 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498111

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498111/0 /scratch/stefan/7787277/working/building/REAL300025498111 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1001)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1001
`/scratch/stefan/7787277/working/3D/1001' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: C=CC(CC)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498111.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498111.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498111/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498111 none C=CC(CC)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 168, 201, 201, 97, 97, 97, 68, 68, 68, 68, 68, 57, 29, 57, 13, 1, 1, 1, 1, 1, 1, 1, 68, 201, 201, 201, 201, 201, 201, 201, 201, 201, 168, 168, 97, 68, 68, 68, 68, 68, 29, 29, 1, 68, 68] 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])
total number of confs: 834
number of broken/clashed sets: 73
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498111 none C=CC(CC)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [1, 1, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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: [31, 30, 19, 30, 30, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 15, 68, 68, 68, 68, 68, 1, 31, 31, 31, 30, 30, 30, 30, 30, 30, 19, 19, 5, 1, 1, 1, 1, 1, 7, 7, 68, 1, 1] 201
rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 45, 40, 46, 41, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 42, 43, 44])
total number of confs: 222
number of broken/clashed sets: 73
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498111 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498111
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498111/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498111
Building REAL300025498112
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498112'
/scratch/stefan/7787277/working/building/REAL300025498112 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498112

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498112/0 /scratch/stefan/7787277/working/building/REAL300025498112 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1002)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1002
`/scratch/stefan/7787277/working/3D/1002' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1)

`REAL300025498112.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498112.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498112/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498112 none CC(C)(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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: [154, 82, 154, 82, 82, 61, 61, 61, 61, 61, 48, 39, 48, 13, 1, 1, 1, 1, 1, 1, 1, 61, 154, 201, 201, 154, 154, 154, 154, 154, 154, 82, 61, 61, 61, 61, 61, 39, 39, 1, 61, 61, 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])
total number of confs: 840
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498112 none CC(C)(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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: [6, 1, 6, 6, 11, 11, 11, 22, 22, 22, 22, 22, 38, 38, 74, 108, 201, 201, 201, 201, 201, 22, 1, 1, 1, 7, 7, 7, 6, 6, 6, 11, 22, 22, 22, 22, 22, 74, 74, 201, 22, 22, 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: 536
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498112 none CC(C)(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1CC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', '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, 1, 1, 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, 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: [9, 4, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 16, 61, 61, 61, 61, 61, 1, 9, 22, 22, 9, 9, 9, 9, 9, 9, 4, 1, 1, 1, 1, 1, 10, 10, 61, 1, 1, 22, 22, 22, 22, 22] 201
rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 40, 21, 41] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44, 45, 46])
total number of confs: 182
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498112 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498112
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498112/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498112
Building REAL300025498113
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498113'
/scratch/stefan/7787277/working/building/REAL300025498113 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498113

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498113/0 /scratch/stefan/7787277/working/building/REAL300025498113 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1003)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1003
`/scratch/stefan/7787277/working/3D/1003' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2C[C@H]3C[C@H]3C2)C1)

`REAL300025498113.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498113.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498113/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498113 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2C[C@H]3C[C@H]3C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [3, 1, 3, 10, 23, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 4, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 1, 10, 10, 76, 1, 1, 1, 1, 1, 4, 22, 22, 22, 22, 22, 22, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 44, 10, 11, 12, 13, 14, 15, 43, 27, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 176
number of broken/clashed sets: 7
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498113 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2C[C@H]3C[C@H]3C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [42, 22, 42, 76, 111, 201, 201, 201, 201, 201, 22, 22, 22, 22, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 76, 76, 201, 22, 22, 22, 22, 22, 9, 1, 1, 1, 1, 1, 1, 22, 22] 201
rigid atoms, others: [37, 38, 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, 43, 44])
total number of confs: 507
number of broken/clashed sets: 7
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498113 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)[C@H]2C[C@H]3C[C@H]3C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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: [59, 35, 12, 1, 1, 1, 1, 1, 1, 1, 59, 76, 76, 76, 76, 76, 113, 113, 113, 201, 201, 201, 201, 201, 201, 201, 201, 76, 35, 35, 1, 76, 76, 76, 76, 76, 113, 201, 201, 201, 201, 201, 201, 76, 76] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 649
number of broken/clashed sets: 7
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498113 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498113
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498113/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498113
Building REAL300025498114
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498114'
/scratch/stefan/7787277/working/building/REAL300025498114 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498114

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498114/0 /scratch/stefan/7787277/working/building/REAL300025498114 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1004)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1004
`/scratch/stefan/7787277/working/3D/1004' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(=O)NC=N1)

`REAL300025498114.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498114.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498114/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498114 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(=O)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [18, 18, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 36, 102, 102, 102, 102, 102, 1, 18, 18, 18, 18, 18, 18, 18, 18, 5, 1, 1, 1, 1, 1, 20, 20, 102, 1, 1, 18, 18] 201
rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11, 40, 21, 39, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42])
total number of confs: 223
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498114 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(=O)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 148, 148, 148, 102, 102, 102, 102, 102, 80, 38, 80, 13, 1, 1, 1, 1, 1, 1, 1, 102, 201, 201, 201, 201, 201, 201, 201, 201, 148, 102, 102, 102, 102, 102, 38, 38, 1, 102, 102, 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])
total number of confs: 572
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498114 none CC1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C(=O)NC=N1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 11, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 52, 52, 106, 141, 201, 201, 201, 201, 201, 18, 1, 1, 1, 1, 1, 2, 2, 2, 6, 18, 18, 18, 18, 18, 106, 106, 201, 18, 18, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 41, 42, 22, 23, 24, 25, 26] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 584
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498114 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498114
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498114/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498114
Building REAL300025498115
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498115'
/scratch/stefan/7787277/working/building/REAL300025498115 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498115

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498115/0 /scratch/stefan/7787277/working/building/REAL300025498115 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1005)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1005
`/scratch/stefan/7787277/working/3D/1005' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC(=O)NC1)

`REAL300025498115.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498115.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498115/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498115 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC(=O)NC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 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: [10, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 14, 29, 82, 82, 82, 82, 82, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 14, 14, 82, 1, 1, 10, 10, 10, 10, 10, 10, 10] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 39, 40, 20, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47])
total number of confs: 172
number of broken/clashed sets: 4
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498115 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC(=O)NC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 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: [201, 123, 123, 123, 82, 82, 82, 82, 82, 70, 39, 70, 13, 1, 1, 1, 1, 1, 1, 1, 82, 201, 201, 201, 201, 201, 201, 201, 201, 201, 123, 82, 82, 82, 82, 82, 39, 39, 1, 82, 82, 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])
total number of confs: 669
number of broken/clashed sets: 4
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498115 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCC(=O)NC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', '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, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 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, 7, 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: [1, 1, 1, 4, 4, 4, 10, 10, 10, 10, 10, 28, 28, 61, 104, 201, 201, 201, 201, 201, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 10, 10, 10, 10, 10, 61, 61, 201, 10, 10, 1, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 41, 42, 43, 44, 45, 46, 47, 21, 22, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 457
number of broken/clashed sets: 4
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498115 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498115
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498115/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498115
Building REAL300025498116
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498116'
/scratch/stefan/7787277/working/building/REAL300025498116 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498116

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498116/0 /scratch/stefan/7787277/working/building/REAL300025498116 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1006)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1006
`/scratch/stefan/7787277/working/3D/1006' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCOC1CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025498116.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498116.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498116/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498116 none CCOC1CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 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, 6, 7, 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: [32, 32, 25, 25, 25, 11, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 17, 63, 63, 63, 63, 63, 1, 25, 32, 32, 32, 32, 32, 25, 25, 25, 25, 11, 11, 2, 1, 1, 1, 1, 1, 8, 8, 63, 1, 1, 25, 25] 201
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49, 50])
total number of confs: 196
number of broken/clashed sets: 121
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498116 none CCOC1CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 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, 6, 7, 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: [201, 201, 201, 201, 201, 178, 63, 63, 63, 63, 63, 63, 63, 63, 50, 29, 50, 13, 1, 1, 1, 1, 1, 1, 1, 63, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 178, 178, 63, 63, 63, 63, 63, 63, 29, 29, 1, 63, 63, 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, 49, 50])
total number of confs: 749
number of broken/clashed sets: 121
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498116 none CCOC1CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 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, 6, 7, 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: [3, 3, 1, 1, 1, 1, 1, 5, 25, 25, 25, 25, 25, 25, 25, 25, 29, 29, 54, 100, 201, 201, 201, 201, 201, 25, 1, 3, 3, 3, 3, 3, 1, 1, 1, 1, 5, 5, 25, 25, 25, 25, 25, 25, 54, 54, 201, 25, 25, 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: 437
number of broken/clashed sets: 121
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498116 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498116
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498116/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498116
Building REAL300025498117
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498117'
/scratch/stefan/7787277/working/building/REAL300025498117 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498117

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498117/0 /scratch/stefan/7787277/working/building/REAL300025498117 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1007)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1007
`/scratch/stefan/7787277/working/3D/1007' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)S1)

`REAL300025498117.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498117.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498117/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498117 none CC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 14, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 32, 55, 143, 143, 143, 143, 143, 1, 11, 11, 11, 11, 11, 11, 5, 1, 1, 1, 1, 1, 32, 32, 143, 1, 1, 11, 11, 11] 201
rigid atoms, others: [32, 33, 34, 38, 6, 7, 8, 9, 10, 11, 12, 22, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42])
total number of confs: 299
number of broken/clashed sets: 23
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498117 none CC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 14, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  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, 143, 143, 143, 143, 143, 103, 41, 103, 13, 1, 1, 1, 1, 1, 1, 1, 143, 201, 201, 201, 201, 201, 201, 200, 143, 143, 143, 143, 143, 41, 41, 1, 143, 143, 201, 201, 201] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 604
number of broken/clashed sets: 23
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498117 none CC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)S1 NO_LONG_NAME
dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 14, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 36, 36, 90, 128, 201, 201, 201, 201, 201, 11, 1, 1, 1, 2, 2, 2, 3, 11, 11, 11, 11, 11, 90, 90, 201, 11, 11, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 548
number of broken/clashed sets: 23
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498117 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498117
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498117/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498117
Building REAL300025498118
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498118'
/scratch/stefan/7787277/working/building/REAL300025498118 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498118

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498118/0 /scratch/stefan/7787277/working/building/REAL300025498118 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1008)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1008
`/scratch/stefan/7787277/working/3D/1008' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CON=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498118.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498118.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498118/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498118 none O=C(CC1=CON=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 12, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 12, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 11, 42, 42, 42, 42, 42, 1, 12, 12, 29, 29, 4, 1, 1, 1, 1, 1, 7, 7, 42, 1, 1] 201
rigid atoms, others: [32, 33, 34, 38, 39, 8, 9, 10, 11, 12, 13, 14, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 35, 36, 37])
total number of confs: 142
number of broken/clashed sets: 2
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498118 none O=C(CC1=CON=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 12, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [63, 63, 63, 121, 201, 201, 201, 201, 42, 42, 42, 42, 42, 40, 38, 40, 13, 1, 1, 1, 1, 1, 1, 1, 42, 121, 121, 201, 201, 63, 42, 42, 42, 42, 42, 38, 38, 1, 42, 42] 201
rigid atoms, others: [37, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39])
total number of confs: 635
number of broken/clashed sets: 2
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498118 none O=C(CC1=CON=C1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 12, 8, 1, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [12, 4, 1, 1, 1, 1, 1, 1, 12, 12, 29, 29, 29, 29, 29, 38, 38, 82, 110, 201, 201, 201, 201, 201, 29, 4, 4, 1, 1, 12, 29, 29, 29, 29, 29, 82, 82, 201, 29, 29] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 549
number of broken/clashed sets: 2
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498118 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498118
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498118/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498118
Building REAL300025498119
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498119'
/scratch/stefan/7787277/working/building/REAL300025498119 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498119

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498119/0 /scratch/stefan/7787277/working/building/REAL300025498119 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1009)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1009
`/scratch/stefan/7787277/working/3D/1009' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CN1C(=O)CC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498119.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498119.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498119/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498119 none CN1C(=O)CC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [13, 13, 13, 13, 13, 13, 4, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 17, 39, 119, 119, 119, 119, 119, 1, 13, 13, 13, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 17, 17, 119, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 44, 10, 11, 12, 13, 14, 15, 16, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 239
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498119 none CN1C(=O)CC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 156, 201, 156, 156, 119, 119, 119, 119, 119, 100, 48, 100, 12, 1, 1, 1, 1, 1, 1, 1, 119, 201, 201, 201, 201, 201, 201, 201, 156, 119, 119, 119, 119, 119, 48, 48, 1, 119, 119] 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, 43, 44])
total number of confs: 662
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498119 none CN1C(=O)CC[C@@H]1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 13, 13, 13, 13, 13, 34, 34, 67, 105, 201, 201, 201, 201, 201, 13, 2, 2, 2, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 67, 67, 201, 13, 13] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 33, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 469
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498119 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498119
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498119/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498119
Building REAL300025498120
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498120'
/scratch/stefan/7787277/working/building/REAL300025498120 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498120

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498120/0 /scratch/stefan/7787277/working/building/REAL300025498120 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1010)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1010
`/scratch/stefan/7787277/working/3D/1010' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C)CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)C1)

`REAL300025498120.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498120.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498120/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498120 none CC1(C)CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 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, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [47, 47, 47, 47, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 9, 49, 49, 49, 49, 49, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 19, 19, 4, 1, 1, 1, 1, 1, 5, 5, 49, 1, 1, 47, 47] 201
rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 40, 46, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 48, 49])
total number of confs: 227
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498120 none CC1(C)CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 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, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 153, 81, 81, 81, 49, 49, 49, 49, 49, 44, 28, 44, 13, 1, 1, 1, 1, 1, 1, 1, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 153, 153, 81, 49, 49, 49, 49, 49, 28, 28, 1, 49, 49, 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: 798
number of broken/clashed sets: 59
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498120 none CC1(C)CC(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 5, 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, 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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 27, 27, 27, 47, 47, 47, 47, 47, 51, 51, 100, 141, 201, 201, 201, 201, 201, 47, 1, 2, 2, 2, 2, 2, 2, 1, 1, 1, 5, 5, 27, 47, 47, 47, 47, 47, 100, 100, 201, 47, 47, 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: 583
number of broken/clashed sets: 59
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498120 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498120
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498120/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498120
Building REAL300025498121
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498121'
/scratch/stefan/7787277/working/building/REAL300025498121 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498121

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498121/0 /scratch/stefan/7787277/working/building/REAL300025498121 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1011)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1011
`/scratch/stefan/7787277/working/3D/1011' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)C1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)OC=C1)

`REAL300025498121.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498121.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498121/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498121 none CC(C)C1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)OC=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.2', 'C.2', 'C.3', '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.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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: [13, 13, 13, 13, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 35, 129, 129, 129, 129, 129, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 17, 17, 129, 1, 1, 13, 13] 201
rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 44, 43, 23, 39] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42, 45, 46])
total number of confs: 231
number of broken/clashed sets: 43
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498121 none CC(C)C1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)OC=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.2', 'C.2', 'C.3', '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.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 179, 179, 179, 129, 129, 129, 129, 129, 80, 31, 80, 13, 1, 1, 1, 1, 1, 1, 1, 129, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 179, 129, 129, 129, 129, 129, 31, 31, 1, 129, 129, 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])
total number of confs: 556
number of broken/clashed sets: 43
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498121 none CC(C)C1=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)OC=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.2', 'C.2', 'C.3', '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.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 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, 4, 4, 4, 13, 13, 13, 13, 13, 45, 45, 89, 132, 201, 201, 201, 201, 201, 13, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 4, 13, 13, 13, 13, 13, 89, 89, 201, 13, 13, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 45, 46, 24, 25, 26, 5, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 527
number of broken/clashed sets: 43
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498121 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498121
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498121/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498121
Building REAL300025498122
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498122'
/scratch/stefan/7787277/working/building/REAL300025498122 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498122

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498122/0 /scratch/stefan/7787277/working/building/REAL300025498122 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1012)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1012
`/scratch/stefan/7787277/working/3D/1012' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C(F)F)CCC2)C1)

`REAL300025498122.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498122.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498122/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498122 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C(F)F)CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 15, 15, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 31, 31, 17, 17, 17, 1, 10, 10, 59, 1, 1, 1, 1, 1, 5, 31, 17, 17, 17, 17, 17, 17, 1, 1] 201
rigid atoms, others: [32, 1, 43, 33, 10, 11, 12, 13, 14, 15, 42, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 212
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498122 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C(F)F)CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 15, 15, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens 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, 60, 89, 193, 193, 193, 193, 193, 17, 17, 17, 17, 7, 7, 1, 7, 1, 1, 6, 6, 1, 1, 1, 17, 60, 60, 193, 17, 17, 17, 17, 17, 7, 6, 1, 1, 1, 1, 1, 1, 17, 17] 201
rigid atoms, others: [36, 37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 472
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498122 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(C(F)F)CCC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 5, 5, 15, 15, 5, 5, 5, 5, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [43, 30, 12, 1, 1, 1, 1, 1, 1, 1, 43, 59, 59, 59, 59, 59, 90, 90, 90, 193, 201, 201, 193, 193, 193, 59, 30, 30, 1, 59, 59, 59, 59, 59, 90, 201, 193, 193, 193, 193, 193, 193, 59, 59] 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: 660
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498122 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498122
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498122/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498122
Building REAL300025498123
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498123'
/scratch/stefan/7787277/working/building/REAL300025498123 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498123

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498123/0 /scratch/stefan/7787277/working/building/REAL300025498123 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1013)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1013
`/scratch/stefan/7787277/working/3D/1013' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CN=CN=C1)

`REAL300025498123.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498123.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498123/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498123 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CN=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 6, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 170, 170, 170, 125, 125, 125, 125, 125, 67, 30, 67, 13, 1, 1, 1, 1, 1, 1, 1, 125, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 170, 125, 125, 125, 125, 125, 30, 30, 1, 125, 125, 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])
total number of confs: 650
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498123 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CN=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 6, 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, 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: [5, 1, 5, 12, 12, 12, 25, 25, 25, 25, 25, 42, 42, 78, 116, 201, 201, 201, 201, 201, 25, 1, 1, 1, 1, 1, 1, 5, 5, 5, 4, 11, 25, 25, 25, 25, 25, 78, 78, 201, 25, 25, 1, 1, 1] 201
rigid atoms, others: [1, 42, 43, 44, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 498
number of broken/clashed sets: 60
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498123 none CC(C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)C1=CN=CN=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 1, 8, 1, 7, 7, 7, 7, 6, 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, 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: [14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 31, 125, 125, 125, 125, 125, 1, 14, 17, 17, 14, 17, 17, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 16, 16, 125, 1, 1, 17, 14, 17] 201
rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 40, 20, 41, 36] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42, 43, 44])
total number of confs: 264
number of broken/clashed sets: 45
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498123 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498123
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498123/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498123
Building REAL300025498124
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498124'
/scratch/stefan/7787277/working/building/REAL300025498124 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498124

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498124/0 /scratch/stefan/7787277/working/building/REAL300025498124 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1014)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1014
`/scratch/stefan/7787277/working/3D/1014' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(F)CCOC2)C1)

`REAL300025498124.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498124.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498124/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498124 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(F)CCOC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 101, 101, 101, 101, 101, 1, 1, 1, 1, 1, 1, 5, 5, 5, 19, 19, 19, 19, 19, 1, 15, 15, 101, 1, 1, 1, 1, 1, 5, 19, 19, 19, 19, 19, 19, 1, 1] 201
rigid atoms, others: [32, 1, 40, 41, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36, 37, 38, 39])
total number of confs: 218
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498124 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(F)CCOC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens 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, 77, 122, 201, 201, 201, 201, 201, 19, 19, 19, 19, 9, 9, 1, 9, 1, 1, 1, 1, 1, 1, 19, 77, 77, 201, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 19, 19] 201
rigid atoms, others: [34, 35, 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, 40, 41])
total number of confs: 498
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498124 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2(F)CCOC2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'F', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 15, 5, 5, 12, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7]
dock color type numbers: [6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [74, 44, 13, 1, 1, 1, 1, 1, 1, 1, 74, 101, 101, 101, 101, 101, 149, 149, 149, 201, 201, 201, 201, 201, 101, 44, 44, 1, 101, 101, 101, 101, 101, 149, 201, 201, 201, 201, 201, 201, 101, 101] 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: 660
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498124 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498124
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498124/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498124
Building REAL300025498125
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498125'
/scratch/stefan/7787277/working/building/REAL300025498125 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498125

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498125/0 /scratch/stefan/7787277/working/building/REAL300025498125 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1015)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1015
`/scratch/stefan/7787277/working/3D/1015' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)N1C)

`REAL300025498125.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498125.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498125/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498125 none CC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 43, 106, 106, 106, 106, 106, 1, 20, 20, 20, 20, 20, 20, 5, 1, 1, 1, 1, 1, 25, 25, 106, 1, 1, 20, 20, 20] 201
rigid atoms, others: [32, 33, 34, 35, 7, 8, 9, 10, 11, 12, 13, 40, 23, 39, 31] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42, 43])
total number of confs: 240
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498125 none CC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 149, 149, 149, 106, 106, 106, 106, 106, 83, 40, 83, 13, 1, 1, 1, 1, 1, 1, 1, 106, 201, 201, 201, 201, 201, 201, 149, 106, 106, 106, 106, 106, 40, 40, 1, 106, 106, 201, 201, 201] 201
rigid atoms, others: [38, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43])
total number of confs: 559
number of broken/clashed sets: 11
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498125 none CC1=NC=C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)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.2', 'C.2', 'C.3', '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.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 8, 5, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
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, 20, 20, 20, 20, 20, 45, 45, 102, 138, 201, 201, 201, 201, 201, 20, 1, 1, 2, 2, 2, 1, 9, 20, 20, 20, 20, 20, 102, 102, 201, 20, 20, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 24, 25, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 585
number of broken/clashed sets: 11
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498125 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498125
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498125/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498125
Building REAL300025498126
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498126'
/scratch/stefan/7787277/working/building/REAL300025498126 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498126

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498126/0 /scratch/stefan/7787277/working/building/REAL300025498126 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1016)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1016
`/scratch/stefan/7787277/working/3D/1016' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC(C)(C)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498126.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498126.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498126/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498126 none CC(C)(C)CCC(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 92, 92, 92, 66, 66, 66, 66, 66, 40, 24, 40, 13, 1, 1, 1, 1, 1, 1, 1, 66, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 92, 66, 66, 66, 66, 66, 24, 24, 1, 66, 66] 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])
total number of confs: 766
number of broken/clashed sets: 41
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498126 none CC(C)(C)CCC(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [22, 22, 22, 22, 22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 21, 66, 66, 66, 66, 66, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 1, 1, 1, 1, 1, 12, 12, 66, 1, 1] 201
rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 189
number of broken/clashed sets: 41
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498126 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498126
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498126/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498126
Building REAL300025498127
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498127'
/scratch/stefan/7787277/working/building/REAL300025498127 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498127

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498127/0 /scratch/stefan/7787277/working/building/REAL300025498127 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1017)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1017
`/scratch/stefan/7787277/working/3D/1017' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NC=N2)C1)

`REAL300025498127.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498127.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498127/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498127 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 21, 45, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 21, 21, 135, 1, 1, 1, 1, 1, 5, 8, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 37, 38, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36])
total number of confs: 253
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498127 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [25, 8, 25, 60, 99, 201, 201, 201, 201, 201, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 60, 60, 201, 8, 8, 8, 8, 8, 3, 1, 1, 1, 8, 8] 201
rigid atoms, others: [34, 35, 36, 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, 37, 38])
total number of confs: 447
number of broken/clashed sets: 33
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498127 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=NC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 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, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [100, 41, 13, 1, 1, 1, 1, 1, 1, 1, 100, 135, 135, 135, 135, 135, 201, 201, 201, 201, 201, 201, 201, 201, 135, 41, 41, 1, 135, 135, 135, 135, 135, 201, 201, 201, 201, 135, 135] 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: 630
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498127 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498127
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498127/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498127
Building REAL300025498128
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498128'
/scratch/stefan/7787277/working/building/REAL300025498128 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498128

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498128/0 /scratch/stefan/7787277/working/building/REAL300025498128 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1018)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1018
`/scratch/stefan/7787277/working/3D/1018' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCCCCC(C)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498128.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498128.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498128/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498128 none CCCCCCC(C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens need rotated
201  conformations in 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, 91, 175, 91, 91, 49, 49, 49, 49, 49, 41, 28, 41, 13, 1, 1, 1, 1, 1, 1, 1, 49, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 175, 175, 175, 175, 91, 49, 49, 49, 49, 49, 28, 28, 1, 49, 49] 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: 810
number of broken/clashed sets: 66
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498128 none CCCCCCC(C)C(=O)NC1C=CCN(C(=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.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 7, 7, 7, 7, 7, 6, 7, 7]
dock color type numbers: [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, 7, 7, 7]
0  hydrogens 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, 16, 5, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 6, 12, 49, 49, 49, 49, 49, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 6, 6, 49, 1, 1] 201
rigid atoms, others: [16, 15, 10, 11, 12, 13, 46, 45, 48, 49, 14, 54, 26, 47, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 50, 51, 52])
total number of confs: 203
number of broken/clashed sets: 66
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498128 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498128
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498128/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498128
Building REAL300025498129
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498129'
/scratch/stefan/7787277/working/building/REAL300025498129 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498129

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498129/0 /scratch/stefan/7787277/working/building/REAL300025498129 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1019)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1019
`/scratch/stefan/7787277/working/3D/1019' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCC1=NC=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498129.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498129.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498129/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498129 none O=C(CCC1=NC=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens 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, 19, 25, 30, 30, 23, 30, 30, 1, 1, 1, 1, 1, 1, 1, 3, 3, 10, 20, 71, 71, 71, 71, 71, 1, 19, 19, 25, 25, 30, 25, 30, 5, 1, 1, 1, 1, 1, 10, 10, 71, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 44, 10, 11, 12, 13, 14, 15, 16, 43, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 246
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498129 none O=C(CCC1=NC=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [110, 110, 110, 190, 201, 201, 201, 200, 201, 201, 71, 71, 71, 71, 71, 57, 29, 57, 13, 1, 1, 1, 1, 1, 1, 1, 71, 190, 190, 201, 201, 201, 201, 201, 110, 71, 71, 71, 71, 71, 29, 29, 1, 71, 71] 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, 43, 44])
total number of confs: 785
number of broken/clashed sets: 71
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498129 none O=C(CCC1=NC=CC=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 1, 8, 1, 1, 1, 8, 8, 5, 1, 1, 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, 6, 7, 7]
dock color type numbers: [6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 5, 4, 1, 1, 1, 1, 1, 1, 1, 9, 9, 14, 14, 14, 14, 14, 22, 22, 65, 112, 201, 201, 201, 201, 201, 14, 5, 5, 4, 4, 1, 1, 1, 9, 14, 14, 14, 14, 14, 65, 65, 201, 14, 14] 201
rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 9, 31] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 490
number of broken/clashed sets: 78
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498129 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498129
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498129/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498129
Building REAL300025498130
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498130'
/scratch/stefan/7787277/working/building/REAL300025498130 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498130

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498130/0 /scratch/stefan/7787277/working/building/REAL300025498130 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1020)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1020
`/scratch/stefan/7787277/working/3D/1020' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=CC=N1)

`REAL300025498130.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498130.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498130/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498130 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 7, 7, 7, 7, 6, 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: [13, 13, 13, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 26, 76, 76, 76, 76, 76, 1, 13, 13, 7, 13, 13, 13, 13, 4, 1, 1, 1, 1, 1, 12, 12, 76, 1, 1, 13, 13] 201
rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 40, 22, 39, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 36, 37, 38, 41, 42])
total number of confs: 168
number of broken/clashed sets: 3
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498130 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 7, 7, 7, 7, 6, 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, 88, 88, 88, 76, 76, 76, 76, 76, 71, 40, 71, 13, 1, 1, 1, 1, 1, 1, 1, 76, 201, 201, 148, 201, 201, 201, 201, 88, 76, 76, 76, 76, 76, 40, 40, 1, 76, 76, 201, 201] 201
rigid atoms, others: [38, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42])
total number of confs: 621
number of broken/clashed sets: 3
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498130 none CC1=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 1, 8, 7, 7, 7, 7, 6, 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, 5, 5, 5, 13, 13, 13, 13, 13, 39, 39, 66, 110, 201, 201, 201, 201, 201, 13, 1, 1, 1, 2, 2, 2, 1, 5, 13, 13, 13, 13, 13, 66, 66, 201, 13, 13, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 41, 42, 23, 24, 25, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 465
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498130 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498130
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498130/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498130
Building REAL300025498131
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498131'
/scratch/stefan/7787277/working/building/REAL300025498131 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498131

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498131/0 /scratch/stefan/7787277/working/building/REAL300025498131 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1021)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1021
`/scratch/stefan/7787277/working/3D/1021' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CC1=CC=CO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498131.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498131.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498131/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498131 none O=C(CC1=CC=CO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 12, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 22, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 22, 88, 88, 88, 88, 88, 1, 22, 22, 26, 26, 26, 5, 1, 1, 1, 1, 1, 13, 13, 88, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 39, 8, 9, 10, 11, 12, 13, 14, 40, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 36, 37, 38])
total number of confs: 222
number of broken/clashed sets: 44
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498131 none O=C(CC1=CC=CO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 12, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [114, 114, 114, 193, 201, 201, 201, 201, 88, 88, 88, 88, 88, 55, 30, 55, 13, 1, 1, 1, 1, 1, 1, 1, 88, 193, 193, 201, 201, 201, 114, 88, 88, 88, 88, 88, 30, 30, 1, 88, 88] 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])
total number of confs: 767
number of broken/clashed sets: 44
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498131 none O=C(CC1=CC=CO1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 1, 1, 1, 1, 12, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 26, 26, 26, 26, 26, 50, 50, 82, 121, 201, 201, 201, 201, 201, 26, 4, 4, 1, 1, 1, 14, 26, 26, 26, 26, 26, 82, 82, 201, 26, 26] 201
rigid atoms, others: [2, 3, 4, 5, 6, 7, 27, 28, 29] set([0, 1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 521
number of broken/clashed sets: 44
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498131 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498131
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498131/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498131
Building REAL300025498132
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498132'
/scratch/stefan/7787277/working/building/REAL300025498132 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498132

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498132/0 /scratch/stefan/7787277/working/building/REAL300025498132 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1022)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1022
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2=NC=CC=N2)C1)

`REAL300025498132.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498132.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498132/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498132 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 5, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 23, 45, 138, 138, 138, 138, 138, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 5, 8, 8, 1, 23, 23, 138, 1, 1, 1, 1, 1, 5, 8, 5, 8, 1, 1] 201
rigid atoms, others: [32, 1, 37, 38, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36])
total number of confs: 267
number of broken/clashed sets: 25
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498132 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 5, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 10, 26, 61, 99, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 10, 61, 61, 201, 10, 10, 10, 10, 10, 4, 1, 1, 1, 10, 10] 201
rigid atoms, others: [34, 35, 36, 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, 37, 38])
total number of confs: 455
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498132 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=CC=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 8, 1, 1, 1, 8, 5, 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, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [100, 48, 13, 1, 1, 1, 1, 1, 1, 1, 100, 138, 138, 138, 138, 138, 201, 201, 201, 201, 201, 201, 201, 201, 138, 48, 48, 1, 138, 138, 138, 138, 138, 201, 201, 201, 201, 138, 138] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 630
number of broken/clashed sets: 25
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498132 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498132
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498132/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498132
Building REAL300025498133
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498133'
/scratch/stefan/7787277/working/building/REAL300025498133 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498133

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498133/0 /scratch/stefan/7787277/working/building/REAL300025498133 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1023)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1023
`/scratch/stefan/7787277/working/3D/1023' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(C)CCC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498133.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498133.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498133/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498133 none CCC(C)CCC(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 127, 201, 127, 46, 46, 46, 43, 43, 43, 43, 43, 38, 24, 38, 13, 1, 1, 1, 1, 1, 1, 1, 43, 201, 201, 201, 201, 201, 201, 201, 201, 201, 129, 129, 127, 127, 46, 43, 43, 43, 43, 43, 24, 24, 1, 43, 43] 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])
total number of confs: 947
number of broken/clashed sets: 77
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498133 none CCC(C)CCC(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 36, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 12, 43, 43, 43, 43, 43, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 22, 22, 18, 18, 3, 1, 1, 1, 1, 1, 6, 6, 43, 1, 1] 201
rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 240
number of broken/clashed sets: 77
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498133 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498133
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498133/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498133
Building REAL300025498134
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498134'
/scratch/stefan/7787277/working/building/REAL300025498134 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025498134

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498134/0 /scratch/stefan/7787277/working/building/REAL300025498134 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1024)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1024
`/scratch/stefan/7787277/working/3D/1024' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3N=CNC3=CC=C2)C1)

`REAL300025498134.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498134.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498134/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498134 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3N=CNC3=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 7, 7, 6, 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, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 21, 47, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 1, 21, 21, 142, 1, 1, 1, 1, 1, 6, 10, 10, 10, 10, 10, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 259
number of broken/clashed sets: 30
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498134 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3N=CNC3=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 7, 7, 6, 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, 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: [31, 10, 31, 64, 110, 201, 201, 201, 201, 201, 10, 10, 10, 10, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 64, 64, 201, 10, 10, 10, 10, 10, 4, 1, 1, 1, 1, 1, 10, 10] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 446
number of broken/clashed sets: 30
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498134 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3N=CNC3=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.2', 'C.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 7, 7, 6, 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, 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: [108, 44, 13, 1, 1, 1, 1, 1, 1, 1, 108, 142, 142, 142, 142, 142, 199, 199, 199, 201, 201, 201, 201, 201, 201, 201, 201, 142, 44, 44, 1, 142, 142, 142, 142, 142, 199, 201, 201, 201, 201, 201, 142, 142] 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: 616
number of broken/clashed sets: 30
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498134 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025498134/1 /scratch/stefan/7787277/working/building/REAL300025498134 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 1025)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1025
`/scratch/stefan/7787277/working/3D/1025' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3NC=NC3=CC=C2)C1)

`REAL300025498134.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025498134.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498134/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498134 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3NC=NC3=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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, 6, 18, 33, 114, 114, 114, 114, 114, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 1, 18, 18, 114, 1, 1, 1, 1, 1, 5, 13, 13, 13, 13, 13, 1, 1] 201
rigid atoms, others: [32, 1, 34, 35, 33, 10, 11, 12, 13, 14, 15, 43, 27, 42, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 36, 37, 38, 39, 40, 41])
total number of confs: 217
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498134 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3NC=NC3=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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: [43, 13, 43, 83, 118, 201, 201, 201, 201, 201, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 83, 83, 201, 13, 13, 13, 13, 13, 5, 1, 1, 1, 1, 1, 13, 13] 201
rigid atoms, others: [37, 38, 39, 40, 41, 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, 42, 43])
total number of confs: 503
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498134 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=C3NC=NC3=CC=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [11, 1, 5, 14, 1, 8, 8, 1, 11, 8, 8, 5, 1, 1, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 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: [80, 45, 13, 1, 1, 1, 1, 1, 1, 1, 80, 114, 114, 114, 114, 114, 158, 158, 158, 201, 201, 201, 201, 201, 201, 201, 201, 114, 45, 45, 1, 114, 114, 114, 114, 114, 158, 201, 201, 201, 201, 201, 114, 114] 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: 578
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498134 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498134
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498134/0.*
1: /scratch/stefan/7787277/working/building/REAL300025498134/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498134
Building REAL300025498135
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498135'
/scratch/stefan/7787277/working/building/REAL300025498135 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498135

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498135/0 /scratch/stefan/7787277/working/building/REAL300025498135 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1026)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1026
`/scratch/stefan/7787277/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)N1CC=CC(NC(=O)C2=CC=CN=N2)C1)

`REAL300025498135.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498135.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498135/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498135 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 5, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [6, 1, 6, 22, 48, 142, 142, 142, 142, 142, 1, 1, 1, 1, 1, 1, 5, 5, 5, 8, 8, 8, 8, 8, 1, 22, 22, 142, 1, 1, 1, 1, 1, 5, 8, 8, 8, 1, 1] 201
rigid atoms, others: [32, 1, 37, 38, 10, 11, 12, 13, 14, 15, 24, 28, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 33, 34, 35, 36])
total number of confs: 263
number of broken/clashed sets: 32
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498135 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 5, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [27, 8, 27, 61, 102, 201, 201, 201, 201, 201, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 61, 61, 201, 8, 8, 8, 8, 8, 3, 1, 1, 1, 8, 8] 201
rigid atoms, others: [34, 35, 36, 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, 37, 38])
total number of confs: 446
number of broken/clashed sets: 32
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498135 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CC=CN=N2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'N.ar', '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, 1, 1, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 5, 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, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [104, 40, 13, 1, 1, 1, 1, 1, 1, 1, 104, 142, 142, 142, 142, 142, 201, 201, 201, 201, 201, 201, 201, 201, 142, 40, 40, 1, 142, 142, 142, 142, 142, 201, 201, 201, 201, 142, 142] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 27] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38])
total number of confs: 611
number of broken/clashed sets: 32
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498135 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498135
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498135/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498135
Building REAL300025498136
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498136'
/scratch/stefan/7787277/working/building/REAL300025498136 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498136

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498136/0 /scratch/stefan/7787277/working/building/REAL300025498136 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1027)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1027
`/scratch/stefan/7787277/working/3D/1027' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1C)

`REAL300025498136.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498136.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498136/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498136 none CCN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1C 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 11, 11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 16, 26, 60, 60, 60, 60, 60, 1, 11, 11, 23, 23, 23, 23, 23, 11, 5, 1, 1, 1, 1, 1, 16, 16, 60, 1, 1, 11, 11, 11] 201
rigid atoms, others: [34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 43, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46])
total number of confs: 216
number of broken/clashed sets: 14
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498136 none CCN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1C 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 108, 108, 108, 108, 66, 66, 66, 60, 60, 60, 60, 60, 56, 37, 56, 13, 1, 1, 1, 1, 1, 1, 1, 60, 108, 108, 201, 201, 201, 201, 201, 108, 66, 60, 60, 60, 60, 60, 37, 37, 1, 60, 60, 108, 108, 108] 201
rigid atoms, others: [41, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46])
total number of confs: 852
number of broken/clashed sets: 14
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498136 none CCN1N=CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1C 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 5, 8, 8, 1, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 5, 5, 5, 11, 11, 11, 11, 11, 25, 25, 42, 66, 108, 108, 108, 108, 108, 11, 1, 1, 5, 5, 5, 5, 5, 1, 5, 11, 11, 11, 11, 11, 42, 42, 108, 11, 11, 2, 2, 2] 201
rigid atoms, others: [32, 1, 2, 3, 4, 5, 6, 25, 26] set([0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46])
total number of confs: 294
number of broken/clashed sets: 14
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498136 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498136
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498136/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498136
Building REAL300025498137
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498137'
/scratch/stefan/7787277/working/building/REAL300025498137 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498137

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498137/0 /scratch/stefan/7787277/working/building/REAL300025498137 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1028)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1028
`/scratch/stefan/7787277/working/3D/1028' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C(C)O1)

`REAL300025498137.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498137.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498137/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498137 none CC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 33, 58, 146, 146, 146, 146, 146, 1, 9, 9, 9, 9, 9, 9, 5, 1, 1, 1, 1, 1, 33, 33, 146, 1, 1, 9, 9, 9] 201
rigid atoms, others: [32, 33, 34, 38, 6, 7, 8, 9, 10, 11, 12, 22, 39, 30, 31] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 35, 36, 37, 40, 41, 42])
total number of confs: 307
number of broken/clashed sets: 26
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498137 none CC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 201, 201, 201, 201, 146, 146, 146, 146, 146, 103, 45, 103, 13, 1, 1, 1, 1, 1, 1, 1, 146, 201, 201, 201, 201, 201, 201, 201, 146, 146, 146, 146, 146, 45, 45, 1, 146, 146, 201, 201, 201] 201
rigid atoms, others: [37, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42])
total number of confs: 592
number of broken/clashed sets: 26
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498137 none CC1=NC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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']
dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 5, 12, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 4, 9, 9, 9, 9, 9, 30, 30, 83, 119, 201, 201, 201, 201, 201, 9, 1, 1, 1, 2, 2, 2, 4, 9, 9, 9, 9, 9, 83, 83, 201, 9, 9, 2, 2, 2] 201
rigid atoms, others: [0, 1, 2, 3, 4, 23, 24, 25] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42])
total number of confs: 537
number of broken/clashed sets: 26
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498137 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498137
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498137/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498137
Building REAL300025498138
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498138'
/scratch/stefan/7787277/working/building/REAL300025498138 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498138

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498138/0 /scratch/stefan/7787277/working/building/REAL300025498138 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1029)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1029
`/scratch/stefan/7787277/working/3D/1029' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC1=NN(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025498138.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498138.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498138/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498138 none CCC1=NN(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [20, 9, 9, 9, 9, 9, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 18, 32, 81, 81, 81, 81, 81, 1, 9, 20, 20, 20, 20, 20, 9, 9, 9, 5, 1, 1, 1, 1, 1, 18, 18, 81, 1, 1, 9] 201
rigid atoms, others: [45, 36, 37, 38, 39, 40, 9, 10, 11, 12, 13, 14, 15, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 46])
total number of confs: 234
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498138 none CCC1=NN(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 130, 130, 130, 130, 130, 94, 94, 94, 81, 81, 81, 81, 81, 69, 39, 69, 13, 1, 1, 1, 1, 1, 1, 1, 81, 130, 201, 201, 201, 201, 201, 130, 130, 130, 94, 81, 81, 81, 81, 81, 39, 39, 1, 81, 81, 130] 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: 804
number of broken/clashed sets: 15
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498138 none CCC1=NN(C)C(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 1, 8, 8, 5, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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: [5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 9, 9, 9, 9, 20, 20, 42, 67, 130, 130, 130, 130, 130, 9, 1, 5, 5, 5, 5, 5, 2, 2, 2, 3, 9, 9, 9, 9, 9, 42, 42, 130, 9, 9, 1] 201
rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 46, 26] set([0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45])
total number of confs: 329
number of broken/clashed sets: 15
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498138 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498138
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498138/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498138
Building REAL300025498139
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498139'
/scratch/stefan/7787277/working/building/REAL300025498139 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498139

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498139/0 /scratch/stefan/7787277/working/building/REAL300025498139 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1030)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1030
`/scratch/stefan/7787277/working/3D/1030' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CCN1C=NN=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498139.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498139.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498139/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498139 none O=C(CCN1C=NN=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 8, 8, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 16, 22, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 25, 79, 79, 79, 79, 79, 1, 16, 16, 22, 22, 35, 4, 1, 1, 1, 1, 1, 15, 15, 79, 1, 1] 201
rigid atoms, others: [32, 33, 34, 35, 36, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38, 39])
total number of confs: 255
number of broken/clashed sets: 67
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498139 none O=C(CCN1C=NN=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 8, 8, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens 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, 201, 201, 201, 79, 79, 79, 79, 79, 45, 27, 45, 12, 1, 1, 1, 1, 1, 1, 1, 79, 195, 195, 201, 201, 201, 95, 79, 79, 79, 79, 79, 27, 27, 1, 79, 79] 201
rigid atoms, others: [39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41])
total number of confs: 739
number of broken/clashed sets: 67
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498139 none O=C(CCN1C=NN=N1)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1 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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [11, 1, 5, 5, 8, 1, 8, 8, 8, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 9, 5, 1, 1, 1, 1, 1, 1, 26, 26, 35, 35, 35, 35, 35, 62, 62, 96, 135, 201, 201, 201, 201, 201, 35, 9, 9, 5, 5, 1, 26, 35, 35, 35, 35, 35, 96, 96, 201, 35, 35] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 30] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 575
number of broken/clashed sets: 67
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498139 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498139
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498139/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498139
Building REAL300025498140
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498140'
/scratch/stefan/7787277/working/building/REAL300025498140 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
2 protomers extracted for REAL300025498140

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498140/0 /scratch/stefan/7787277/working/building/REAL300025498140 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1031)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1031
`/scratch/stefan/7787277/working/3D/1031' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC[NH+](CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1)

`REAL300025498140.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498140.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498140/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498140 none CC1CC[NH+](CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [20, 20, 20, 20, 15, 20, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 10, 21, 21, 21, 21, 21, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 15, 15, 5, 1, 1, 1, 1, 1, 6, 6, 21, 1, 1, 20, 20, 20, 20] 56
rigid atoms, others: [43, 39, 40, 9, 10, 11, 12, 13, 14, 15, 48, 41, 25, 47, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46, 49, 50, 51, 52])
total number of confs: 113
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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498140 none CC1CC[NH+](CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [56, 56, 56, 56, 53, 56, 35, 35, 35, 21, 21, 21, 21, 21, 18, 16, 18, 10, 1, 1, 1, 1, 1, 1, 1, 21, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 53, 53, 35, 21, 21, 21, 21, 21, 16, 16, 1, 21, 21, 56, 56, 56, 56] 56
rigid atoms, others: [46, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51, 52])
total number of confs: 213
number of broken/clashed sets: 39
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498140 none CC1CC[NH+](CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7]
dock color type numbers: [7, 7, 7, 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]
0  hydrogens need rotated
56  conformations in input
total number of sets (complete confs): 56
using faster count positions algorithm for large data
unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 9, 20, 20, 20, 20, 20, 28, 28, 38, 41, 56, 56, 56, 56, 56, 20, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 3, 3, 9, 20, 20, 20, 20, 20, 38, 38, 56, 20, 20, 1, 1, 1, 1] 56
rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 51, 34, 49, 50, 35, 52, 26, 27, 5, 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: 171
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498140 /scratch/stefan/7787277/working /scratch/stefan/7787277
mkdir: created directory `1'
/scratch/stefan/7787277/working/building/REAL300025498140/1 /scratch/stefan/7787277/working/building/REAL300025498140 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 1 (index: 1032)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1032
`/scratch/stefan/7787277/working/3D/1032' -> `1.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CCN(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1)

`REAL300025498140.mol2' -> `1.mol2'
`temp.mol2' -> `REAL300025498140.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498140/1/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`1.mol2' -> `1.mol2.original'
`output.mol2' -> `1.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498140 none CC1CCN(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [24, 24, 24, 24, 19, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 13, 25, 59, 59, 59, 59, 59, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 19, 19, 4, 1, 1, 1, 1, 1, 13, 13, 59, 1, 1, 24, 24, 24, 24] 201
rigid atoms, others: [38, 39, 8, 9, 10, 11, 12, 13, 14, 47, 40, 46, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43, 44, 45, 48, 49, 50, 51])
total number of confs: 192
number of broken/clashed sets: 24
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498140 none CC1CCN(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 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]
0  hydrogens need rotated
201  conformations 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, 108, 108, 108, 59, 59, 59, 59, 59, 41, 19, 41, 11, 1, 1, 1, 1, 1, 1, 1, 59, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 197, 197, 108, 59, 59, 59, 59, 59, 19, 19, 1, 59, 59, 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])
total number of confs: 746
number of broken/clashed sets: 24
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498140 none CC1CCN(CC(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CC1 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.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H']
dock atom type numbers: [5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 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]
0  hydrogens need rotated
201  conformations in input
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, 14, 14, 14, 24, 24, 24, 24, 24, 47, 47, 78, 121, 201, 201, 201, 201, 201, 24, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 6, 6, 14, 24, 24, 24, 24, 24, 78, 78, 201, 24, 24, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 34, 48, 49, 50, 51, 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: 523
number of broken/clashed sets: 24
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498140 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498140
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498140/0.*
1: /scratch/stefan/7787277/working/building/REAL300025498140/1.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498140
Building REAL300025498141
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498141'
/scratch/stefan/7787277/working/building/REAL300025498141 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498141

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498141/0 /scratch/stefan/7787277/working/building/REAL300025498141 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1033)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1033
`/scratch/stefan/7787277/working/3D/1033' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=CC=C2F)C1)

`REAL300025498141.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498141.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498141/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498141 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=CC=C2F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 15, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 20, 42, 135, 135, 135, 135, 135, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 1, 20, 20, 135, 1, 1, 1, 1, 1, 4, 11, 11, 11, 1, 1] 201
rigid atoms, others: [32, 1, 38, 33, 10, 11, 12, 13, 14, 15, 39, 25, 29, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 34, 35, 36, 37])
total number of confs: 253
number of broken/clashed sets: 33
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498141 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=CC=C2F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 15, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [32, 11, 32, 69, 118, 201, 201, 201, 201, 201, 11, 11, 11, 11, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 11, 69, 69, 201, 11, 11, 11, 11, 11, 6, 1, 1, 1, 11, 11] 201
rigid atoms, others: [35, 36, 37, 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, 38, 39])
total number of confs: 472
number of broken/clashed sets: 33
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498141 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=NC=CC=C2F)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', '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, 1, 1, 5, 8, 1, 11, 1, 8, 1, 1, 1, 1, 15, 5, 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, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 43, 13, 1, 1, 1, 1, 1, 1, 1, 99, 135, 135, 135, 135, 135, 194, 194, 194, 201, 201, 201, 201, 201, 201, 135, 43, 43, 1, 135, 135, 135, 135, 135, 194, 201, 201, 201, 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])
total number of confs: 598
number of broken/clashed sets: 33
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498141 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498141
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498141/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498141
Building REAL300025498142
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498142'
/scratch/stefan/7787277/working/building/REAL300025498142 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498142

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498142/0 /scratch/stefan/7787277/working/building/REAL300025498142 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1034)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1034
`/scratch/stefan/7787277/working/3D/1034' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1OCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498142.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498142.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498142/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498142 none CC1OCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [8, 8, 8, 8, 8, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 63, 170, 170, 170, 170, 170, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 1, 1, 1, 1, 1, 24, 24, 170, 1, 1] 201
rigid atoms, others: [35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 44, 43, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 40, 41, 42])
total number of confs: 315
number of broken/clashed sets: 50
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498142 none CC1OCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in 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, 169, 169, 169, 169, 169, 133, 66, 133, 13, 1, 1, 1, 1, 1, 1, 1, 169, 201, 201, 201, 201, 201, 201, 201, 201, 201, 195, 169, 169, 169, 169, 169, 66, 66, 1, 169, 169] 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])
total number of confs: 601
number of broken/clashed sets: 50
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498142 none CC1OCCC1C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)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.2', 'C.2', 'C.3', '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']
dock atom type numbers: [5, 5, 12, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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]
0  hydrogens need rotated
201  conformations in input
total 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, 8, 8, 8, 8, 8, 19, 19, 54, 109, 201, 201, 201, 201, 201, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 54, 54, 201, 8, 8] 201
rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 33, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 441
number of broken/clashed sets: 50
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498142 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498142
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498142/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498142
Building REAL300025498143
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498143'
/scratch/stefan/7787277/working/building/REAL300025498143 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498143

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498143/0 /scratch/stefan/7787277/working/building/REAL300025498143 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1035)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1035
`/scratch/stefan/7787277/working/3D/1035' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCOC1)

`REAL300025498143.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498143.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498143/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498143 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 6, 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, 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: [14, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 34, 104, 104, 104, 104, 104, 1, 14, 14, 14, 14, 14, 14, 14, 5, 1, 1, 1, 1, 1, 17, 17, 104, 1, 1, 14, 14, 14, 14, 14, 14] 201
rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 37, 20, 38, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 39, 40, 41, 42, 43, 44])
total number of confs: 223
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498143 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 6, 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, 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, 133, 133, 133, 104, 104, 104, 104, 104, 81, 46, 81, 13, 1, 1, 1, 1, 1, 1, 1, 104, 201, 201, 201, 201, 201, 201, 201, 133, 104, 104, 104, 104, 104, 46, 46, 1, 104, 104, 201, 201, 201, 201, 201, 201] 201
rigid atoms, others: [36, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44])
total number of confs: 636
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498143 none CC1(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCOC1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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']
dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 5, 5, 12, 5, 7, 7, 7, 6, 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, 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, 5, 5, 5, 14, 14, 14, 14, 14, 35, 35, 69, 116, 201, 201, 201, 201, 201, 14, 1, 1, 1, 1, 2, 2, 2, 5, 14, 14, 14, 14, 14, 69, 69, 201, 14, 14, 1, 1, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 39, 40, 41, 42, 43, 44, 21, 22, 23, 24] set([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])
total number of confs: 490
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498143 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498143
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498143/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498143
Building REAL300025498144
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498144'
/scratch/stefan/7787277/working/building/REAL300025498144 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498144

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498144/0 /scratch/stefan/7787277/working/building/REAL300025498144 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1036)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1036
`/scratch/stefan/7787277/working/3D/1036' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN(C(F)F)N=C2)C1)

`REAL300025498144.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498144.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498144/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498144 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN(C(F)F)N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'F', 'F', 'N.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 5, 15, 15, 8, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need 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, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 12, 36, 36, 12, 12, 1, 9, 9, 76, 1, 1, 1, 1, 1, 5, 12, 36, 12, 1, 1] 201
rigid atoms, others: [32, 1, 34, 33, 40, 10, 11, 12, 13, 14, 15, 39, 26, 30, 31] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 35, 36, 37, 38])
total number of confs: 239
number of broken/clashed sets: 13
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498144 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN(C(F)F)N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'F', 'F', 'N.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 5, 15, 15, 8, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [26, 12, 26, 56, 82, 201, 201, 201, 201, 201, 12, 12, 12, 12, 5, 5, 1, 5, 1, 1, 1, 1, 7, 7, 1, 1, 12, 56, 56, 201, 12, 12, 12, 12, 12, 5, 1, 7, 1, 12, 12] 201
rigid atoms, others: [36, 38, 16, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 39, 40])
total number of confs: 457
number of broken/clashed sets: 13
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498144 none O=C(CSC1=NNC(=O)[N-]1)N1CC=CC(NC(=O)C2=CN(C(F)F)N=C2)C1 NO_LONG_NAME
dock atom types: ['O.2', 'C.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'F', 'F', 'N.2', 'C.2', '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, 1, 1, 5, 8, 1, 11, 1, 1, 8, 5, 15, 15, 8, 1, 5, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 37, 13, 1, 1, 1, 1, 1, 1, 1, 57, 76, 76, 76, 76, 76, 109, 109, 109, 201, 201, 201, 201, 201, 201, 201, 76, 37, 37, 1, 76, 76, 76, 76, 76, 109, 201, 201, 201, 76, 76] 201
rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40])
total number of confs: 491
number of broken/clashed sets: 13
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498144 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498144
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498144/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498144
Building REAL300025498145
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498145'
/scratch/stefan/7787277/working/building/REAL300025498145 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498145

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498145/0 /scratch/stefan/7787277/working/building/REAL300025498145 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1037)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1037
`/scratch/stefan/7787277/working/3D/1037' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: NC(=O)C1=CNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1)

`REAL300025498145.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498145.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498145/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498145 none NC(=O)C1=CNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 11, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 6, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 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]
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: [26, 16, 26, 16, 16, 16, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 43, 111, 111, 111, 111, 111, 1, 16, 26, 26, 16, 16, 4, 1, 1, 1, 1, 1, 23, 23, 111, 1, 1, 16] 200
rigid atoms, others: [32, 33, 34, 35, 36, 40, 9, 10, 11, 12, 13, 14, 15, 41, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 37, 38, 39, 42])
total number of confs: 277
number of broken/clashed sets: 10
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498145 none NC(=O)C1=CNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 11, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 6, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 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]
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: [200, 156, 200, 156, 156, 156, 127, 127, 127, 111, 111, 111, 111, 111, 93, 40, 93, 13, 1, 1, 1, 1, 1, 1, 1, 111, 156, 200, 200, 156, 156, 127, 111, 111, 111, 111, 111, 40, 40, 1, 111, 111, 156] 200
rigid atoms, others: [39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42])
total number of confs: 621
number of broken/clashed sets: 10
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498145 none NC(=O)C1=CNC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)=C1 NO_LONG_NAME
dock atom types: ['N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.3', 'C.2', 'N.2', 'N.am', 'C.2', 'O.2', 'N.2', '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, 11, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 5, 8, 1, 11, 5, 14, 1, 8, 8, 1, 11, 8, 5, 1, 6, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7]
dock color type numbers: [4, 7, 6, 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]
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: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 16, 16, 16, 47, 47, 79, 102, 156, 156, 156, 156, 156, 16, 1, 3, 3, 1, 1, 7, 16, 16, 16, 16, 16, 79, 79, 156, 16, 16, 1] 200
rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 26, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41])
total number of confs: 414
number of broken/clashed sets: 10
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498145 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498145
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498145/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498145
Building REAL300025498146
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498146'
/scratch/stefan/7787277/working/building/REAL300025498146 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498146

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498146/0 /scratch/stefan/7787277/working/building/REAL300025498146 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1038)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1038
`/scratch/stefan/7787277/working/3D/1038' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC)(CC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498146.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498146.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498146/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498146 none CCC(CC)(CC)C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
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, 7, 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, 8, 8, 8, 1, 8, 8] 8
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])
total number of confs: 14
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: REAL300025498146 none CCC(CC)(CC)C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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
8  conformations in input
total number of sets (complete confs): 8
using default count positions algorithm for smaller data
unique positions, atoms: [5, 5, 4, 5, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 8, 8, 8, 8, 8, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 1, 1, 1, 1, 1, 6, 6, 8, 1, 1] 8
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49])
total number of confs: 35
number of broken/clashed sets: 3
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498146 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498146
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498146/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498146
Building REAL300025498147
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498147'
/scratch/stefan/7787277/working/building/REAL300025498147 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498147

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498147/0 /scratch/stefan/7787277/working/building/REAL300025498147 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1039)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1039
`/scratch/stefan/7787277/working/3D/1039' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCO1)

`REAL300025498147.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498147.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498147/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498147 none CC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 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, 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: [22, 22, 22, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 34, 80, 80, 80, 80, 80, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 5, 1, 1, 1, 1, 1, 20, 20, 80, 1, 1, 22, 22, 22, 22] 201
rigid atoms, others: [34, 35, 36, 37, 6, 7, 8, 9, 10, 11, 12, 43, 22, 38, 42] set([0, 1, 2, 3, 4, 5, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 39, 40, 41, 44, 45, 46, 47])
total number of confs: 218
number of broken/clashed sets: 19
./output.2.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498147 none CC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 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, 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, 105, 105, 105, 80, 80, 80, 80, 80, 67, 39, 67, 13, 1, 1, 1, 1, 1, 1, 1, 80, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 105, 80, 80, 80, 80, 80, 39, 39, 1, 80, 80, 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])
total number of confs: 643
number of broken/clashed sets: 19
./output.3.db2in.mol2.db2.gz file written out
Cleaning up
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498147 none CC1CC(C(=O)NC2C=CCN(C(=O)CSC3=NNC(=O)[N-]3)C2)CCO1 NO_LONG_NAME
dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', 'N.am', 'C.2', '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, 1, 1, 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, 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, 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, 7, 7, 7, 22, 22, 22, 22, 22, 48, 48, 97, 136, 201, 201, 201, 201, 201, 22, 1, 1, 1, 2, 2, 2, 1, 1, 1, 1, 7, 22, 22, 22, 22, 22, 97, 97, 201, 22, 22, 1, 1, 1, 1] 201
rigid atoms, others: [0, 1, 2, 3, 4, 32, 44, 45, 46, 47, 23, 24, 25, 29, 30, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43])
total number of confs: 562
number of broken/clashed sets: 19
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498147 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498147
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498147/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498147
Building REAL300025498148
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498148'
/scratch/stefan/7787277/working/building/REAL300025498148 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498148

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498148/0 /scratch/stefan/7787277/working/building/REAL300025498148 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1040)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1040
`/scratch/stefan/7787277/working/3D/1040' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCCC(C)(CC)C(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498148.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498148.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498148/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498148 none CCCC(C)(CC)C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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, 197, 183, 137, 183, 183, 180, 137, 137, 109, 109, 109, 109, 109, 65, 30, 65, 13, 1, 1, 1, 1, 1, 1, 1, 109, 201, 201, 201, 201, 201, 201, 201, 183, 183, 183, 184, 184, 184, 184, 184, 137, 109, 109, 109, 109, 109, 30, 30, 1, 109, 109] 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])
total number of confs: 786
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: REAL300025498148 none CCCC(C)(CC)C(=O)NC1C=CCN(C(=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.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.3', '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, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 7, 7, 7, 7, 7, 7, 7, 6, 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: [20, 19, 12, 5, 12, 12, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 34, 109, 109, 109, 109, 109, 1, 20, 20, 20, 20, 20, 20, 20, 12, 12, 12, 16, 16, 16, 16, 16, 5, 1, 1, 1, 1, 1, 16, 16, 109, 1, 1] 201
rigid atoms, others: [45, 43, 9, 10, 11, 12, 13, 14, 44, 50, 51, 46, 25, 15, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 47, 48, 49])
total number of confs: 310
number of broken/clashed sets: 39
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498148 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498148
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498148/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498148
Building REAL300025498149
mkdir: created directory `/scratch/stefan/7787277/working/building/REAL300025498149'
/scratch/stefan/7787277/working/building/REAL300025498149 /scratch/stefan/7787277/working /scratch/stefan/7787277
Extracting previously generated protomers and correcting pH mod types
1 protomers extracted for REAL300025498149

mkdir: created directory `0'
/scratch/stefan/7787277/working/building/REAL300025498149/0 /scratch/stefan/7787277/working/building/REAL300025498149 /scratch/stefan/7787277/working /scratch/stefan/7787277
Protomer 0 (index: 1041)
Found valid previously generated 3D confromation in /scratch/stefan/7787277/working/3D/1041
`/scratch/stefan/7787277/working/3D/1041' -> `0.mol2'
Preparing input files

Starting the preparation of the solvation calculations (AMSOL7.1)
  (SMILES: CCC(CC)CC(=O)NC1C=CCN(C(=O)CSC2=NNC(=O)[N-]2)C1)

`REAL300025498149.mol2' -> `0.mol2'
`temp.mol2' -> `REAL300025498149.mol2'
antechamber (part of ambertools (downloadable for free!)) is not available on your computer
obabel might write out a warning since atom types cannot be translated/interpreted correctly.
The obabel warnings can be confidently disregarded. They don't affect the docking.
1 molecule converted
 running AMSOL7.1: SM5.42R (in water solvent) 
 running AMSOL7.1: SM5.42R (in hexane solvent) 
`/scratch/stefan/7787277/working/building/REAL300025498149/0/temp.mol2' -> `temp-working.mol2'
`temp-working.mol2' -> `temp.mol2'
`0.mol2' -> `0.mol2.original'
`output.mol2' -> `0.mol2'
WARNING:root:Setting energy window to 12 and max confs to 200
('energy: ', 12.0)
('conf: ', 200)
['output.1.db2in.mol2', 'output.2.db2in.mol2']
verbose debugging requested.
{'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'}
names: REAL300025498149 none CCC(CC)CC(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens need rotated
201  conformations in input
total number of sets (complete confs): 201
using faster count positions algorithm for large data
unique positions, atoms: [201, 201, 195, 201, 201, 79, 79, 79, 54, 54, 54, 54, 54, 46, 28, 46, 13, 1, 1, 1, 1, 1, 1, 1, 54, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 195, 195, 79, 54, 54, 54, 54, 54, 28, 28, 1, 54, 54] 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])
total number of confs: 810
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: REAL300025498149 none CCC(CC)CC(=O)NC1C=CCN(C(=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.2', 'C.2', 'C.3', '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, 5, 5, 5, 1, 11, 8, 5, 1, 1, 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, 6, 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, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7]
0  hydrogens 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, 21, 27, 27, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 13, 54, 54, 54, 54, 54, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 21, 21, 5, 1, 1, 1, 1, 1, 7, 7, 54, 1, 1] 201
rigid atoms, others: [43, 39, 8, 9, 10, 11, 12, 13, 14, 47, 48, 40, 41, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 44, 45, 46])
total number of confs: 183
number of broken/clashed sets: 71
./output.1.db2in.mol2.db2.gz file written out
Cleaning up
/scratch/stefan/7787277/working/building/REAL300025498149 /scratch/stefan/7787277/working /scratch/stefan/7787277

Finished preparing REAL300025498149
Recording results
/scratch/stefan/7787277/working /scratch/stefan/7787277
Appending to /scratch/stefan/7787277/finished/xaaabsm.*
0: /scratch/stefan/7787277/working/building/REAL300025498149/0.*
Removing working files in /scratch/stefan/7787277/working/building/REAL300025498149
/scratch/stefan/7787277
Compressing combined databse files
/scratch/stefan/7787277/finished/xaaabsm.db2.gz
/scratch/stefan/7787277/finished/xaaabsm.solv.gz


=======================================================
WARNING: STORE_PROTOMERS not executable or a directory!
All results left in place (/scratch/stefan/7787277/finished)
=======================================================

Finalizing...
removed `/scratch/stefan/7787277/working/3D/1042'
removed directory: `/scratch/stefan/7787277/working/3D'
`/scratch/stefan/7787277/working/protonate' -> `/scratch/stefan/7787277/archive'
`/scratch/stefan/7787277/working/input-smiles.ism' -> `/scratch/stefan/7787277/archive/input-smiles.ism'
rmdir: removing directory, `/scratch/stefan/7787277/working/building'
rmdir: removing directory, `/scratch/stefan/7787277/working'
ls: No match.
ls: No match.